|
| Status |
Public on Aug 13, 2007 |
| Title |
Zebrafish-control siRNA |
| Sample type |
RNA |
| |
|
| Source name |
24 hours post-fertilization embryos
|
| Organism |
Danio rerio |
| Characteristics |
the embryos injected with the control siRNA
|
| Treatment protocol |
Selected embryos were transferred to 2 mL Eppendorf tube, rinsed with DEPC-treated water. After discarding water, the Trizol solution (GibcoBRL) was added to Eppendorf tube containing embryos.
|
| Growth protocol |
Zebrafish embryos were maintained at 28 ± 0.5 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Fifteen microgram aliquants of the fragmented cRNA were hybridized with the D. rerio Genome AFF-F0027 GeneChip® microarray (Affymetrix, CA) in hybridization cocktail. Hybridization was allowed to proceed overnight (16 h) at 45 °C
|
| Scan protocol |
The distribution of fluorescent material on the array was obtained using GeneChip® Scanner 3000 (Affymetrix, CA)
|
| Description |
Gene expression data from the embryos injected with the control siRNA
|
| Data processing |
The scanned images were firstly assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. A global scaling factor of 500 was used to normalize the different arrays. The differentially expressed genes were judged according to change p-value calculated by GCOS 1.4, and 2-fold change as an empirical criterion.
|
| |
|
| Submission date |
Aug 08, 2007 |
| Last update date |
Jan 04, 2012 |
| Contact name |
M X Chang |
| E-mail(s) |
mingxianchang@ihb.ac.cn
|
| Organization name |
Institute of Hydrobiology, Chinese Academy of Sciences
|
| Lab |
Laboratory of Fish Diseases
|
| Street address |
Luojiaashan
|
| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE8724 |
Gene expression analysis in the zebrafish embryos silenced by zfPGRP-SC |
|
