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Series GSE25245 Query DataSets for GSE25245
Status Public on Jun 06, 2011
Title Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site
Organism Fundulus heteroclitus
Experiment type Expression profiling by array
Summary This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle. At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation.
 
Overall design A loop design was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores. We used three loops in which each loop consisted of Cy3- and Cy5-labeled embryo aRNAs from 12 samples: one sample from each population-treatment-time combination. Within a population-treatment-time, embryos were randomly assigned to one of the three loops. In total, 36 embryos were hybridized to 36 microarrays. The loops formed were SC5C→ SC5P → NBH5C→ NBH5P →SC10C→ SC10P→ NBH10C→ NBH10P → SC15C→ SC15P → NBH15C → NBH15P → SC5C, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological sample at the head of the arrow labeled with Cy5. SC represents the Scorton Creek, Sandwich, MA population (reference), NBH represents the New Bedford Harbor, MA population, C represents control dose (DMSO), P represents the PCB-126 dose, 5 represents 5 dpf, 10 represents 10 dpf and 15 represents 15 dpf.
 
Contributor(s) Oleksiak MF, Karchner SI, Jenny MJ, Franks DG, Mark Welch DB, Hahn ME
Citation(s) 21609454
Submission date Nov 09, 2010
Last update date Jun 05, 2013
Contact name Marjorie F. Oleksiak
E-mail(s) moleksiak@rsmas.miami.edu
Organization name University of Miami
Department Marine Biology and Fisheries
Street address 4600 Rickenbacker Causeway
City Miami
State/province FL
ZIP/Postal code 33149
Country USA
 
Platforms (1)
GPL10430 Rosenstiel Fundulus heteroclitus 7K array
Samples (72)
GSM621147 5 dpf DMSO_embryo_SC1_Cy3
GSM621148 5 DPF PCB-126_embryo_SC4_Cy5
GSM621149 5 DPF PCB-126_embryo_SC4_Cy3
Relations
BioProject PRJNA134661

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25245_RAW.tar 18.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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