Transcriptomics

Dataset Information

3

Environmentally relevant concentrations of the flame retardant BDE-209 in sediment cause minimal effects on Zebrafish embryos.


ABSTRACT: Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects. Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). The RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer. Total RNA was stored at -80oC until analyzed with oligonucleotide microarrays. Zebrafish 44,000 gene arrays (Agilent Single Color 19161, Platform number GPL6457) were purchased from Agilent (Sta. Clara, CA, USA). The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations. Four controls and four treated samples were analyzed, each sample consisting of a pool of embryos. One ug of total RNA was used for all hybridizations. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA). An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA) was used to scan microarray images at 5 μm resolution. Data were resolved from microarray images using Agilent Feature Extraction software and analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA).

ORGANISM(S): Danio rerio  

SUBMITTER: Edward Perkins   Lynn Escalon  Demetrio Raldua  Patrick Babin  Eva Prats  Natalia Vinas 

PROVIDER: E-GEOD-39169 | ArrayExpress | 2013-01-01

SECONDARY ACCESSION(S): GSE39169PRJNA170169

REPOSITORIES: GEO, ArrayExpress

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