title: Ecotoxicogenomics: Microarray interlaboratory comparability.
abstract: Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories with estuarine amphipods exposed to cyfluthrin-spiked or control sediments (10 days). Two sample types were generated, one consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the other consisted of exposed and control whole body amphipods (WB) from which each laboratory extracted RNA. Our findings indicate that gene expression microarray results are repeatable. Differentially expressed data had a higher degree of repeatability across all laboratories in samples with similar RNA quality (Ex) when compared to WB samples with more variable RNA quality. Despite such variability a subset of genes were consistently identified as differentially expressed across all laboratories and sample types. We found that the differences among the individual laboratory results can be attributed to several factors including RNA quality and technical expertise, but the overall results can be improved by following consistent protocols and with appropriate training.
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA, USA. Electronic address: dorisv@sccwrp.org.
authors.forename: Doris E
authors.initials: DE
authors.lastname: Vidal-Dorsch
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA, USA.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Bay
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA, USA.
authors.forename: Shelly
authors.initials: S
authors.lastname: Moore
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA, USA.
authors.forename: Blythe
authors.initials: B
authors.lastname: Layton
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, CA, USA.
authors.forename: Alvine C
authors.initials: AC
authors.lastname: Mehinto
authors.affiliation: University of California, Berkeley, Berkeley, CA, USA.
authors.forename: Chris D
authors.initials: CD
authors.lastname: Vulpe
authors.affiliation: University of California, Berkeley, Berkeley, CA, USA.
authors.forename: Marianna
authors.initials: M
authors.lastname: Brown-Augustine
authors.affiliation: University of California, Berkeley, Berkeley, CA, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Loguinov
authors.affiliation: University of Massachusetts Boston, Boston, MA, USA.
authors.forename: Helen
authors.initials: H
authors.lastname: Poynton
authors.affiliation: Mississippi State University, Starkville, MS, USA; US Army Engineer Research and Development Center, Vicksburg, MS, USA.
authors.forename: Natàlia
authors.initials: N
authors.lastname: Garcia-Reyero
authors.affiliation: US Army Engineer Research and Development Center, Vicksburg, MS, USA.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Perkins
authors.affiliation: US Army Engineer Research and Development Center, Vicksburg, MS, USA.
authors.forename: Lynn
authors.initials: L
authors.lastname: Escalon
authors.affiliation: University of Florida, Gainesville, FL, USA.
authors.forename: Nancy D
authors.initials: ND
authors.lastname: Denslow
authors.affiliation: University of Florida, Gainesville, FL, USA; Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Mexico.
authors.forename: Colli-Dula R
authors.initials: CD
authors.lastname: Cristina
authors.affiliation: Agilent Technologies, Santa Clara, CA, USA.
authors.forename: Tri
authors.initials: T
authors.lastname: Doan
authors.affiliation: Agilent Technologies, Santa Clara, CA, USA; Strand Scientific Intelligence Inc., San Francisco, CA, USA.
authors.forename: Shweta
authors.initials: S
authors.lastname: Shukradas
authors.affiliation: Environment Canada, North Vancouver, B.C., Canada.
authors.forename: Joy
authors.initials: J
authors.lastname: Bruno
authors.affiliation: Environment Canada, North Vancouver, B.C., Canada.
authors.forename: Lorraine
authors.initials: L
authors.lastname: Brown
authors.affiliation: Environment Canada, North Vancouver, B.C., Canada.
authors.forename: Graham
authors.initials: G
authors.lastname: Van Agglen
authors.affiliation: Environment Canada, Moncton, NB, Canada.
authors.forename: Paula
authors.initials: P
authors.lastname: Jackman
authors.affiliation: Environment Canada, Moncton, NB, Canada.
authors.forename: Megan
authors.initials: M
authors.lastname: Bauer
mesh_terms: D033304:Amphipoda / Q000187:drug effects / Q000235:genetics; D000818:Animals; D054750:Ecotoxicology / Q000592:standards*; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D019015:Geologic Sediments / Q000737:chemistry; D006801:Humans; D007753:Laboratories / Q000592:standards*; D009570:Nitriles / Q000633:toxicity; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D011722:Pyrethrins / Q000633:toxicity; D015203:Reproducibility of Results; D043922:Toxicogenetics / Q000592:standards*
chemical_list: D009570:Nitriles; D011722:Pyrethrins; C052570:cyfluthrin
keywords: Amphipod; Ecotoxicogenomics; Gene expression; Inter- and intra-laboratory reproducibility; Intercalibration; Microarray