|
| Status |
Public on Oct 27, 2009 |
| Title |
5d, pineal, night, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
5d old, pineal gland, night-time
|
| Organism |
Danio rerio |
| Characteristics |
Embryo
|
| Growth protocol |
Adults and embryos were kept at 28.5oC under a 14-hr-light/10-hr-dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA was prepared using the Ovation Biotin system kit (NeuGen) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
2.2 micrograms of labeled cDNA was hybridized to the Affymetrix zebrafish GeneChip at 45 degrees C for 18 hrs. Post-hybridization, staining, and washing were performed using a Fluidics Station 450 (Affymetrix) with protocol EukGE-WS2v4_450.
|
| Scan protocol |
The hybridized chips were scanned by Affymetrix GeneChip Scanner 3000 and then processed with GeneChip Operating Software (GCOS).
|
| Description |
Biological replicate 3 of 4
|
| Data processing |
Global scaling was employed for analysis and the target Intensity value (TGT) was set as 500 following the manufacturer's (Affymetrix) recommendations. GeneChip Operating Software (Affymetrix) was used to create CEL files from each experiment. Further statistical analysis was done using JMP, the statistical Discovery Software (http://www.jmp.com).
|
| |
|
| Submission date |
Oct 27, 2008 |
| Last update date |
Oct 27, 2008 |
| Contact name |
Reiko Toyama |
| E-mail(s) |
toyamar@mail.nih.gov
|
| Phone |
301-496-9689
|
| Fax |
301-496-0243
|
| Organization name |
NIH
|
| Department |
NICHD
|
| Lab |
Lab. of Molecular Genetics
|
| Street address |
Bldg.6B, Room 420, 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE13371 |
Transcriptome analysis of the zebrafish pineal gland |
|
