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| Status |
Public on Dec 31, 2011 |
| Title |
Interlaboratory study to determine the reproducibility of toxicogenomics datasets |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, toxicogenomics predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we aimed to determine whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test sites adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen B[a]P and the human hepatocyte cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were still observed between the test sites, a common subset of B[a]P responsive genes was identified across all test sites which included both genes previously reported in the literature as B[a]P responsive in addition to the same most highly up and down regulated genes. Pending further analysis, these preliminary data show promise that the current generation of microarray technology in combination with a standard in vitro experimental design can produce robust data that can be reproducibly generated in independent laboratories. Future work will need to determine whether in vitro model(s) can be not only reproducible but also predictive for a range of toxic chemicals with different mechanisms of action. Such an approach may potentially be part of future in vitro testing regimes for regulatory risk assessment.
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| Overall design |
The aim of this study was to evaluate the inter- and intra-laboratory reproducibility of toxicogenomics data for toxicity testing in a regulatory setting. 3 Test Centres performed the same experimental protocol treating HepG2 cells with 3 mM Benzo[a]pyrene (B[a]P) (in 0.5% DMSO) for 24 hours prior to RNA extraction and microarray analysis. Three biological replicates of B[a]P and DMSO treatments were analysed by microarray analysis in each Test Centre. Two Test Centres analysed one sample in triplicate to determine technical reproducibility of the chosen array platform. One Centre analysed two samples in duplicate. 24 samples in total were used in this study
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| Contributor(s) |
Scott DJ, Devonshire A, Adeleye Y, Bennett A, Gribaldo L, Rodrigues R, Sacco MG, Fabbri M, Wilkes T, Schutte M, Foy C, White A |
| Citation(s) |
21871943 |
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| Submission date |
Dec 08, 2010 |
| Last update date |
Feb 22, 2018 |
| Contact name |
Yeyejide A Adeleye |
| E-mail(s) |
yeyejide.adeleye@unilever.com
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| Organization name |
Unilever
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| Street address |
Colworth Science Park
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| City |
Sharnbrook |
| State/province |
Bedfordshire |
| ZIP/Postal code |
MK44 1LQ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL4133 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) |
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| Samples (24)
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| GSM637410 |
B[a]P_Test Centre1_BioRep3_TechRepNA |
| GSM637411 |
DMSO_Test Centre1_BioRep3_TechRepNA |
| GSM637412 |
DMSO_Test Centre1_BioRep2_TechRepNA |
| GSM637413 |
B[a]P_Test Centre1_BioRep2_TechRepNA |
| GSM637414 |
DMSO_Test Centre1_BioRep1_TechRepNA |
| GSM637415 |
B[a]P_Test Centre1_BioRep1_TechRepA |
| GSM637416 |
B[a]P_Test Centre1_BioRep1_TechRepB |
| GSM637417 |
B[a]P_Test Centre1_BioRep1_TechRepC |
| GSM637418 |
B[a]P_Test Centre2_BioRep3_TechRepA |
| GSM637419 |
DMSO_Test Centre2_BioRep3_TechRepA |
| GSM637420 |
B[a]P_Test Centre2_BioRep3_TechRepB |
| GSM637421 |
DMSO_Test Centre2_BioRep3_TechRepB |
| GSM637422 |
DMSO_Test Centre2_BioRep1_TechRepNA |
| GSM637423 |
B[a]P_Test Centre2_BioRep1_TechRepNA |
| GSM637424 |
DMSO_Test Centre2_BioRep2_TechRepNA |
| GSM637425 |
B[a]P_Test Centre2_BioRep2_TechRepNA |
| GSM637426 |
DMSO_Test Centre3_BioRep1_TechRepNA |
| GSM637427 |
DMSO_Test Centre3_BioRep2_TechRepNA |
| GSM637428 |
DMSO_Test Centre3_BioRep3_TechRepNA |
| GSM637429 |
B[a]P_Test Centre3_BioRep1_TechRepNA |
| GSM637430 |
B[a]P_Test Centre3_BioRep2_TechRepA |
| GSM637431 |
B[a]P_Test Centre3_BioRep2_TechRepB |
| GSM637432 |
B[a]P_Test Centre3_BioRep2_TechRepC |
| GSM637433 |
B[a]P_Test Centre3_BioRep3_TechRepNA |
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| Relations |
| BioProject |
PRJNA135687 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE25936_RAW.tar |
112.2 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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