|
| Status |
Public on Oct 01, 2011 |
| Title |
12 hpf control [miRNA] |
| Sample type |
RNA |
| |
|
| Source name |
whole embryo 12 hpf
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tropical 5D
agent: control
dose: n/a
locomotion phenotype: Normal
collection time: 12 hpf
|
| Treatment protocol |
Groups of embryos were waterborne exposed to 300 mM ethanol (absolute ethyl alcohol USP, 200 proof) in buffered embryo medium or 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 at 12, 24, 36, or 48 hpf.
|
| 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 |
miRNA was isolated using a miRNeasy kit (Qiagen) from pooled tissue (75 embryos) harvested at 12-48 hpf (n=2).
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications.
|
| |
|
| Hybridization protocol |
cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications. Labeled cDNA samples were hybridized to miRZebrafish arrays (probe content reflects miRBase release 12.0) and images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).
|
| Scan protocol |
cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications. Labeled cDNA samples were hybridized to miRZebrafish arrays (probe content reflects miRBase release 12.0) and images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).
|
| Description |
This sample is comprised of 75 pooled embryos exposed to embryo medium control from 4-12 hpf and harvested at 12 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.
Raw data file: 07_Z12.0_090073-0126.txt
|
| Data processing |
Data were background-subtracted, normalized by LOWESS (Locally-weighted Regression), and analyzed for differential expression by t-test (p<0.05). Data processing was performed by LC Sciences using proprietary software (Bolstad, BM et al. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193).
|
| |
|
| Submission date |
Jul 12, 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 |
GPL13832 |
| Series (1) |
| GSE30497 |
mRNA and miRNA expression analysis of developmental ethanol exposure in zebrafish |
|
