|
| Status |
Public on Oct 01, 2011 |
| Title |
24 hpf control rep 1 [mRNA] |
| Sample type |
RNA |
| |
|
| Source name |
whole embryo 24 hpf
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tropical 5D
agent: control
dose: n/a
locomotion phenotype: Normal
collection time: 24 hpf
|
| Treatment protocol |
Groups of embryos were waterborne exposed to 0-300 mM ethanol (absolute ethyl alcohol USP, 200 proof) in buffered embryo mediumor embryo medium alone in 20-ml glass vials sealed with Teflon-lined lids to prevent volatilization. Each exposure group was considered a single replicate. Based on previous studies, embryos were exposed to ethanol from 4-24 hpf, rinsed and embryo homogenate was collected.
|
| Growth protocol |
Adult Tropical 5D strain zebrafish (Danio rerio) were raised according to Institutional Animal Care and Use Committee protocols in the Sinnhuber Aquatic Research Laboratory at Oregon State University. Adults were maintained on a 14 h light/10 h dark schedule on a recirculating system in which water was maintained at 28±1 °C with a pH of 7.0±0.2. Following adult spawns, embryos were collected, rinsed, and housed at 28±1 °C in pools of 75 embryos until the start of the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was isolated using TRIzol Reagent from pools of 75 embryos at 24 hpf that were exposed to 100-300 mM ethanol or embryo medium control from 4-24 hpf (n=4). Sample clean-up was performed using MinElute columns.
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis, labeling and hybridization were performed by the University of Idaho Initiative for Bioinformatics and Evolutionary Studies core facility according to NimbleGen microarray protocol v.5.0 with the exception of the first-strand synthesis step in which 50µM oligo (dT) per reaction and 400 ng of random hexamers per µL of reaction were used.
|
| |
|
| Hybridization protocol |
cDNA synthesis, labeling and hybridization were performed by the University of Idaho Initiative for Bioinformatics and Evolutionary Studies core facility according to NimbleGen microarray protocol v.5.0 with the exception of the first-strand synthesis step in which 50µM oligo (dT) per reaction and 400 ng of random hexamers per µL of reaction were used.
|
| Scan protocol |
Labeled cDNA samples were hybridized to a zebrafish 12x135K Nimblegen array and arrays were scanned at 532 pmt. NimbleScan software was used for image analysis.
|
| Description |
This sample is of 75 pooled embryos exposed to embryo medium control from 4-24 hpf. It is the first of four biological replicates used in this experiment, each from pools of embryos.
Raw data file: control rep 1_395174genepixA01_2010-08-06_7092010_532-alligned.pair
|
| Data processing |
NimbleScan software was used for image analysis and quality control. Raw intensity data were quantile normalized by RMA summarization and outliers were identified by correlation analysis based on Pearson correlation coefficient. A single replicate was removed from the 100mM treatment group and resulting data were subject to both pairwise analysis of variance with Tukey's post hoc test and 5% false discovery rate calculation.
|
| |
|
| Submission date |
Jul 07, 2011 |
| Last update date |
Oct 01, 2011 |
| Contact name |
Robert L Tanguay |
| E-mail(s) |
robert.tanguay@oregonstate.edu
|
| Phone |
541-737-6514
|
| Organization name |
Oregon State University
|
| Department |
EMT
|
| Street address |
1007 ALS
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL13318 |
| Series (1) |
| GSE30497 |
mRNA and miRNA expression analysis of developmental ethanol exposure in zebrafish |
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