biomedical and healthCAre Data Discovery Index Ecosystem
biomedical and healthCAre Data Discovery Index Ecosystem
| Title: | Expression Profiles of HepG2 cells treated with genotoxic and non-genotoxic agents
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| dateReleased: |
08-02-2012
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| description: |
The lack of accurate in vitro assays for predicting in vivo toxicity of chemicals together with new legislations demanding replacement and reduction of animal testing has triggered the development of alternative methods. This study aimed at developing a transcriptomics-based in vitro prediction assay for in vivo genotoxicity. The transcriptomics changes induced in the human liver cell line HepG2 by 34 compounds after treatment for 12h, 24h and 48h were used for the selection of gene-sets that can discriminate between in vivo genotoxins (GTX) and in vivo non-genotoxins (NGTX). By combining publicly available results for these chemicals from standard in vitro genotoxicity studies with transcriptomics, we developed several prediction models. These models were validated by means of an additional set of 28 chemicals. The study investigated differential gene expression in HepG2 cell line mRNA following 12 hours of exposure to 34 different compounds and their solvents; 24 and 48 hours of exposure to 62 different compounds and their solvents. Three biological replicates per compound/solvent. In total 560 arrays .
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| privacy: |
not applicable
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| aggregation: |
instance of dataset
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| ID: |
E-GEOD-28878
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| refinement: |
raw
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| alternateIdentifiers: |
28878
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| keywords: |
functional genomics
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| dateModified: |
11-12-2012
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| creators: |
Christina Magkoufopoulou
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| availability: |
available
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| types: |
gene expression
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| name: |
Homo sapiens
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| ID: |
A-GEOD-9101
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| name: |
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (MBNI v11 Entrez Gene ID CDF)
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| accessURL: | https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28878/E-GEOD-28878.raw.1.zip |
| storedIn: |
ArrayExpress
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| qualifier: |
gzip compressed
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| format: |
TXT
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| accessType: |
download
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| authentication: |
none
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| authorization: |
none
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| accessURL: | https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28878/E-GEOD-28878.processed.1.zip |
| storedIn: |
ArrayExpress
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| qualifier: |
gzip compressed
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| format: |
TXT
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| accessType: |
download
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| authentication: |
none
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| authorization: |
none
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| accessURL: | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28878 |
| storedIn: |
Gene Expression Omnibus
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| qualifier: |
not compressed
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| format: |
HTML
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| accessType: |
landing page
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| primary: |
true
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| authentication: |
none
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| authorization: |
none
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| abbreviation: |
EBI
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| homePage: | http://www.ebi.ac.uk/ |
| ID: |
SCR:004727
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| name: |
European Bioinformatics Institute
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| homePage: | https://www.ebi.ac.uk/arrayexpress/ |
| ID: |
SCR:002964
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| name: |
ArrayExpress
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