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Status |
Public on Sep 01, 2013 |
Title |
Prim-5_0.625mM MTBE, bio rep 3 |
Sample type |
RNA |
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Source name |
embryo at Prim-5_exposed to 0.625mM MTBE
|
Organism |
Danio rerio |
Characteristics |
tissue: whole embryo lysate genotype: Tg(fli1a:EGFP)y1 developmental stage: Prim-5; ~30hpf exposed to: 0.625mM MTBE
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Treatment protocol |
Staged (1K cell stage) embryos were randomly assiged to a experimental group consisting of a time point and treatment. Each group consisted of 15 embryos which were pooled for 1 experimental replicate, with three replicates for each experimental group. Treatment with 0.00625, 0.625, 5mM MTBE or control was in a sealed glass vial beginning at approximately 3 hours post fertilization and ending at the assigned time point. Upon completion of the exposure, embryos were snap frozen in liquid nitrogen and stored at -80C until RNA was extracted.
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Growth protocol |
Embryos were maintained at 25C for the duration of exposure.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA extractions: RNeasy Mini Kit 250 (p/n 74106) with on-column DNase treatment (RNAse-free DNAse set, 50 rxn, p/n 79254); Reverse transcription and amplification: NuGEN WT-Ovation™ Pico System (p/n 3300-60); cDNA cleanup by Zymo Research DNA Clean & Concentrator -25 kit (p/n D4006).
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Label |
biotin
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Label protocol |
Fragmentation and biotinylation: NuGEN Encore™ Biotin Module (p/n 4200-60) according to the manufacturer.
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Hybridization protocol |
Hybridizations were performed in an Affymetrix GeneChip Hybridization Oven 640, washing and staining on the Affymetrix Fluidics Station 450 using the GCOS software and protocol EukGE-WS2V4_450.
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Scan protocol |
Scanning on the Affymetrix GeneChip Scanner using GCOS software and according to standard Affymetrix protocols.
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Description |
30_MC.CEL gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at Prim-5
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Data processing |
Agilent Technologies GeneSpring GX software
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Submission date |
Apr 25, 2013 |
Last update date |
Sep 01, 2013 |
Contact name |
Josephine Ann Bonventre |
Organization name |
Oregon State University
|
Department |
Environmental & Molecular Toxicology
|
Lab |
Harper
|
Street address |
1011 Agriculture & Life Sciences Building
|
City |
Corvallis |
State/province |
OR |
ZIP/Postal code |
97331 |
Country |
USA |
|
|
Platform ID |
GPL1319 |
Series (1) |
GSE46371 |
Expression data from zebrafish (Danio rerio) embryos exposed to methyl tert-butyl ether |
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