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Title: Ecotoxicogenomics: interlaboratory comparability of microarray data [LabB_Ex]      
dateReleased:
01-26-2015
description:
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. 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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-64204
refinement:
raw
alternateIdentifiers:
64204
keywords:
functional genomics
dateModified:
02-03-2015
availability:
available
types:
gene expression
name:
Eohaustorius estuarius
ID:
A-GEOD-19554
name:
Agilent-042708 Eohaustorius estuarius EE_Microarray_DV (Probe Name version)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-64204/E-GEOD-64204.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-64204/E-GEOD-64204.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64204
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress