|
| Status |
Public on Apr 09, 2008 |
| Title |
Danio_Brain_Control_3 (X2BC3) |
| Sample type |
RNA |
| |
|
| Source name |
Brain
|
| Organism |
Danio rerio |
| Characteristics |
Strain: Scientific Hatcheries, Sex: Female, N: 3 fish, Birthdate: 8172005, Start date: 432006, Mean Mass: 452.8, Mean Length: 26.4, Mean SGR: 0.148, Mean GSI: 0.123
|
| Treatment protocol |
Groups of eight females of the same age were randomly assigned to each of twelve 3-L tanks (10 cm wide x 15 cm tall x 25 cm deep) arranged on the same shelf of a flow-through rearing system. Test tanks were assigned to starved or control treatments in an alternating manner so that treatments were uniformly distributed across fish ages and tank location. Fish in the starved treatment received no food for 21 days, while fish in the control treatment continued to be fed to apparent satiety three times daily.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA) following the manufacturer's protocol. After extraction, RNA from three fish was pooled for each tank for analysis.
|
| Label |
Biotin
|
| Label protocol |
For each array, up to 10 ug of total RNA were converted to cDNA. Biotinylated cRNA was then produced in vitro using the GeneChip Expression 3' amplification one-cycle target labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Microarrays were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 r.p.m.), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody. This was followed by another round of SAPE prior to scanning using a GeneChip Scanner 3000 (Affymetrix).
|
| Scan protocol |
Scanned using a GeneChip Scanner 3000 (Affymetrix).
|
| Description |
X2BC3
|
| Data processing |
All analyses of microarray data were conducted using Bioconductor for R (www.R-project.org). Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues. The microarray data were filtered as described by Robison et al. (2008). Filtered probesets were then normalized using Robust Multiarray Average (RMA).
|
| |
|
| Submission date |
Apr 09, 2008 |
| Last update date |
Apr 09, 2008 |
| Contact name |
Robert Edward Drew |
| E-mail(s) |
rdrew@uidaho.edu
|
| Phone |
208-885-8478
|
| Fax |
208-885-7905
|
| Organization name |
University of Idaho
|
| Department |
Biological Sciences
|
| Lab |
Robison
|
| Street address |
Life Sciences South Rm 252
|
| City |
Moscow |
| State/province |
ID |
| ZIP/Postal code |
83844-3051 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE11107 |
Effect of starvation on the transcriptomes of the brain and liver in adult female zebrafish (Danio rerio) |
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