|
| Status |
Public on May 01, 2009 |
| Title |
Pineal_DD_ZT2b |
| Sample type |
RNA |
| |
|
| Source name |
pineal at ZT2b, constant darkness
|
| Organism |
Danio rerio |
| Characteristics |
Tg(aanat2:EGFP)Y8 transgenic zebrafish
Age: adult (3-6 months)
Gender: males and females
|
| Treatment protocol |
Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. 12 pineal glands were collected and pooled at each time point and at each light condition.
|
| Growth protocol |
Adult zebrafish were raised in a light- and temperature-controlled recirculation water system under a 12-h light/12-h dark cycle at 28 °C and fed twice a day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, Qiagen).
|
| Label |
biotin
|
| Label protocol |
Double-strand cDNA was generated from 10-100 ng of mRNA by using a T7-linked oligo(dT) primer (Affymetrix). After second-strand synthesis, in vitro transcription was performed with MEGAscript® T7 Kit (Ambion, Inc.). The cRNA (600ng) was then used for second cycle first-strand cDNA (Affymetrix) by using a T7-linked oligo(dT) primer (Affymetrix). After 2nd cycle - second-strand synthesis, in vitro transcription was again performed; this time biotinylated UTP and CTP (Affymetrix) were incorporated in the cRNA, resulting in approximately 1800-fold amplification of labeled RNA.
|
| |
|
| Hybridization protocol |
The target cRNA generated from each sample was fragmented and 15 micogram of the fragmented cRNA was added to the hybridization cocktail which includes in addition to the fragmented target, probe array controls (pre-mixed biotin-labeled bioB, bioC, bioD and cre, in staggered concentrations, ready to be added directly to the hybridization cocktail. These controls facilitate monitoring of the hybridization process for troubleshooting), BSA, and herring sperm DNA. It was then hybridized to the probe array during a 16-hour incubation at 45 deg (C). The array was then washed and stained on the Affymetrix fluidic station (using Streptavidin-Phycoerythrin which binds to the biotinylated UTP and CTP incorporated previously in the hybridized cRNA).
|
| Scan protocol |
The stained array was scanned on the Affymetrix scanner (450).
|
| Description |
Gene expression data from zebrafish pineal
|
| Data processing |
The GCOS (Gene Operating System) generates the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).
|
| |
|
| Submission date |
Oct 14, 2008 |
| Last update date |
Oct 14, 2008 |
| Contact name |
Yoav Gothilf |
| E-mail(s) |
YoavG@tauex.tau.ac.il
|
| Phone |
+972-3-640-6329
|
| Fax |
+972-3-640-6329
|
| Organization name |
Tel Aviv University
|
| Department |
Neurobiology, Faculty of Life Sciences
|
| Lab |
Gothilf
|
| Street address |
Sherman Building, Room 405
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE13196 |
Expression data from zebrafish pineal gland |
|
