|
| Status |
Public on Sep 01, 2013 |
| Title |
Prim-5_5mM MTBE, bio rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
embryo at Prim-5_exposed to 5mM MTBE
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo lysate
genotype: Tg(fli1a:EGFP)y1
developmental stage: Prim-5; ~30hpf
exposed to: 5mM MTBE
|
| 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.
|
| Growth protocol |
Embryos were maintained at 25C for the duration of exposure.
|
| 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).
|
| Label |
biotin
|
| Label protocol |
Fragmentation and biotinylation: NuGEN Encore™ Biotin Module (p/n 4200-60) according to the manufacturer.
|
| |
|
| 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.
|
| Scan protocol |
Scanning on the Affymetrix GeneChip Scanner using GCOS software and according to standard Affymetrix protocols.
|
| Description |
30_HA.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at Prim-5
|
| Data processing |
Agilent Technologies GeneSpring GX software
|
| |
|
| 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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