|
| Status |
Public on Jan 26, 2015 |
| Title |
Ecotoxicogenomics: interlaboratory comparability of microarray data [LabA_WB] |
| Organism |
Eohaustorius estuarius |
| Experiment type |
Expression profiling by array
|
| Summary |
Additional toxicity testing and regulation are needed as the number of compounds chronically released into aquatic coastal environments increases. Decision makers require comprehensive and efficient screening tools to detect adverse biological effects and to identify their cause. Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, identifying sub-lethal organismal responses and identifying contaminant classes underlying observed toxicity. Before transcriptomic information is used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps that impact the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories. Estuarine amphipods were exposed to cyfluthrin-spiked or control sediments for 10 days. Two sample types were generated: the first consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the second type consisted of exposed and control whole body amphipods (WB) from which RNA was extracted by each laboratory. A subset of genes were consistently identified as differentially expressed across all laboratories and sample types. Genes with the highest magnitude of differential expression (> 2 fold) were more likely to be consistently identified as differentially expressed across laboratories. Differentially expressed data had a higher degree of concordance across all laboratories (W = 0.7) in samples with similar RNA quality (Ex) when compared to WB samples (W = 0.5). Our results revealed that several factors can affect data comparability including RNA sample preparation, labeling, instrumentation and technical expertise.
|
| |
|
| Overall design |
First dataset: RNA extracts (Ex) derived from whole bodies of 8 controls and 8 cyfluthrin-exposed amphipods were prepared by one single lab and analyzed (i.e., labeling, microarray hybridization and feature extraction) by all 6 laboratories.
Second dataset: Each of the 6 labs received 8 control and 8 cyfluthrin-exposed whole body samples (WB) for RNA extraction and microarrays. Lab C was unable to analyze the WB samples and only submitted data for the Ex samples.
|
| |
|
| Contributor(s) |
Vidal-Dorsch D, Bay S, Moore S, Layton B, Mehinto A, Vulpe C, Brown-Augustine M, Loguinov A, Poynton H, Garcia-Reyero N, Perkins E, Escalon L, Denslow N, Colli-Dula C, Doan T, Shukradas S, Bruno J, Brown L, Van Agglen G, Jackman P, Bauer M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Dec 15, 2014 |
| Last update date |
Jan 27, 2015 |
| Contact name |
Alvine C Mehinto |
| Organization name |
Southern California Coastal Water Research Project
|
| Lab |
Center for Envirom & Human Toxicol
|
| Street address |
3535 Harbor Blvd, Suite 110
|
| City |
Costa Mesa |
| ZIP/Postal code |
92626 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19554 |
Agilent-042708 Eohaustorius estuarius EE_Microarray_DV (Probe Name version) |
|
| Samples (16)
|
|
| This SubSeries is part of SuperSeries: |
| GSE64213 |
Ecotoxicogenomics: interlaboratory comparability of microarray data |
|
| Relations |
| BioProject |
PRJNA270521 |
Less...
More...