|
| Status |
Public on Feb 29, 2008 |
| Title |
3dpa con 2 |
| Sample type |
RNA |
| |
|
| Source name |
3 day post amputation fin; Vehicle Exposed; replicate 2
|
| Organism |
Danio rerio |
| Characteristics |
AB strain larval zebrafish - regenerating caudal fin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated and the animals were exposed to either DMSO (vehicle control) or 0.5ng/mL TCDD (>99% pure, Chemsyn, Lenexa, KS) in the water for 1 hr. After several rinses in TCDD free water, the larvae were reared until 2 and 3 days post amputation (dpa) when their regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point and treatment, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).
|
| Label |
Labeling and probe processing was conducted under manufactures recommendations.
|
| Label protocol |
A total of 100ng of RNA from the larval fin tissue (+/-TCDD) at 2 and 3 dpa were used to generate biotinylated complementary RNA (cRNA) using the Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Hybridization was conducted as stipulated by Affymetrix GeneChip Expression Analysis Technical Manual (701021 Rev. 5).
|
| Scan protocol |
Affymetrix fluidics station 400 was used to wash the arrays. Arrays were scanned with an Affymetrix scanner 3000.
|
| Description |
The caudal fin of zebrafish larvae at 2day post fertilization were amputated, follwed by exposure with TCDD or vehicle. Regenerating fin tissue was collected at 2 and 3 days post amputation for mRNA abundance analysis.
|
| Data processing |
Data was GC-RMA preprocessed and each gene was normalized to the median using Gene Spring 7.1 software.
|
| |
|
| Submission date |
Jan 15, 2008 |
| Last update date |
Feb 28, 2008 |
| 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 |
GPL1319 |
| Series (1) |
| GSE10184 |
2 or 3 Day Post Amputation Vehicle or TCDD Exposed |
|
| Relations |
| Reanalyzed by |
GSM269747 |
