|
| Status |
Public on Sep 12, 2007 |
| Title |
embryonic hearts, vehicle control treatment, T12h, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish embryonic heart at the age of 84hpf old
|
| Organism |
Danio rerio |
| Characteristics |
Genotype: cmlc2::GFP transgenic zebrafish
|
| Treatment protocol |
For Retinoic Acid treatment, 72 hpf old zebrafish embryos were treated with 1μM all-trans retinoic acid in 0.1% DMSO or 0.1% DMSO continously until the timepoint for heart extraction. For TCDD treatment, 72 hpf old zebrafish embryos were treated with 1ng/μl TCDD in 0.1% DMSO or 0.1% DMSO as a vehicle control for 1 h.
|
| Growth protocol |
All zebrafish embryos were kept at 27ºC in egg water with a 14-h/ 10-h light/dark cycle until the designated age for experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish embryonic heart extraction: 200 cmlc2::GFP transgenic embryos were collected in a 1.5 ml Eppendorf tube with 1 ml L-15/10%FBS media and passed through a 19.5 gauge needle connected to a 10 ml syringe 60 times, thus internal organs were separated from the body by shear force. Fluorescent hearts that specifically expressing GFP were identified and picked up under a fluorescence dissecting scope.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned in an Aglient Gene Array Scanner
|
| Description |
Gene expression data of zebrafish embryonic hearts extracted from 84 hpf old embryos at 12 h post 1h-TCDD dosing
|
| Data processing |
All .cel images were pre-processed with the GC-RMA function in the ArrayAssist Express Version 4.0 software. The output signal intensity for each probeset ID was log2 transformed.
|
| |
|
| Submission date |
Sep 12, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Jing Chen |
| E-mail(s) |
chen12@wisc.edu
|
| Phone |
6082624525
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
pharmaceutical Sciences
|
| Street address |
777 Highland Ave
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE9020 |
Comparative Genomics Identifies Gene Targets for Retinoic Acid in the Embryonic Zebrafish Hearts |
|
