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SRP150704
Mus musculus
54 Downloadable Samples
Illumina HiSeq 2000
Description
The study aimed to investigate genome-wide transcriptome changes in response to L-lactate in primary neuron cultures.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Rattus norvegicus
- 134 Downloadable Samples
UNKNOWN
Description
BACKGROUND: The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of microarray data from untreated or vehicle-treated animals within the control arm of toxicogenomics studies could yield useful information on baseline fluctuations in gene expression, although control animal data has not been available on a scale and in a form best served for data-mining. RESULTS: A dataset of control animal microarray expression data was assembled by a working group of the Health and Environmental Sciences Institute's Technical Committee on the Application of Genomics in Mechanism Based Risk Assessment in order to provide a public resource for assessments of variability in baseline gene expression. Data from over 500 Affymetrix microarrays from control rat liver and kidney were collected from 16 different institutions. Thirty-five biological and technical factors were obtained for each animal, describing a wide range of study characteristics, and a subset were evaluated in detail for their contribution to total variability using multivariate statistical and graphical techniques. CONCLUSIONS: The study factors that emerged as key sources of variability included gender, organ section, strain, and fasting state. These and other study factors were identified as key descriptors that should be included in the minimal information about a toxicogenomics study needed for interpretation of results by an independent source. Genes that are the most and least variable, gender-selective, or altered by fasting were also identified and functionally categorized. Better characterization of gene expression variability in control animals will aid in the design of toxicogenomics studies and in the interpretation of their results. [based on information contained in Final_HESI_Decoder_483_05_015_07.txt provided by CEBS database]
Publication Title
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 62 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Murine Genome U74A Array (mgu74a), UNKNOWN, Affymetrix Murine 11K SubB Array (mu11ksubb), Affymetrix Murine 11K SubA Array (mu11ksuba)
Description
Mouse lymphoma L5178Y cells are treated with Mitomycin C [CAS:50-07-7;CHEBI:27504] and harvested at 4 and 24 hours for analysis.
Publication Title
The Utility of DNA Microarrays for Characterizing Genotoxicity
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Disease, Disease stage, Compound, Time
View Samples- Mus musculus
- 58 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Murine Genome U74A Array (mgu74a), UNKNOWN
Description
Mouse lymphoma L5178Y cells are treated with Taxol (Paclitaxel) [CAS:33069-62-4;CHEBI:7887] and harvested at 4 and 24 hours for analysis.
Publication Title
Toxicogenomics in Risk Assessment: An Overview of an HESI Collaborative Research Program
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Disease, Disease stage, Compound, Time
View Samples- Mus musculus, Homo sapiens
- 59 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Murine Genome U74A Array (mgu74a), Affymetrix Human Genome U95A Array (hgu95a)
Description
Mouse lymphoma L5178Y and Human TK6 cells are treated with Methylmethane Sulfonate [CAS:66-27-3;CHEBI:25255] and harvested a 4 and 24 hours for analysis.
Publication Title
The Utility of DNA Microarrays for Characterizing Genotoxicity
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Disease, Disease stage, Compound, Time
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Mouse lymphoma L5178Y cells are treated with Etoposide [CAS:33419-42-0;CHEBI:4911] and harvested a 4 and 24 hours for analysis.
Publication Title
Toxicogenomics in Risk Assessment: An Overview of an HESI Collaborative Research Program
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Disease, Disease stage, Compound, Time
View Samples- Mus musculus
- 2 Downloadable Samples
- UNKNOWN
Description
Mouse lymphoma L5178Y cells are treated with 4-NitroQuinoline N-Oxide (4-NQO) [CAS:56-57-5;CHEBI:16907] and harvested at 4 and 24 hours for analysis.
Publication Title
The Utility of DNA Microarrays for Characterizing Genotoxicity
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Disease, Disease stage, Compound, Time
View Samples- Triticum aestivum
- 36 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Transcripomic analysis of leaf gene expression in S and N-deficient winter wheat during grain development. Tissue was harvested at anthesis and 7, 14 and 21 days post anthesis from experimental field plots.
Publication Title
Co-ordinated expression of amino acid metabolism in response to N and S deficiency during wheat grain filling.
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject, Time
View Samples- Rattus norvegicus
- 549 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.
Publication Title
Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part, Compound, Time
View Samples- Rattus norvegicus
- 546 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.
Publication Title
Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Compound, Time
View Samples