|
| Status |
Public on Aug 18, 2012 |
| Title |
rainbowtrout_feed_3 |
| Sample type |
RNA |
| |
|
| Source name |
feed
|
| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: muscle
|
| Growth protocol |
Fish were fed ad libitum once a week (RF, restricted feed group) or fed ad libitum twice per day (control) for 1 month.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fish muscles using the RNeasy Mini Kit.
|
| Label |
Cy3
|
| Label protocol |
The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.
|
| |
|
| Hybridization protocol |
After hybridization cocktails preparation, the Agilent 4x44 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.
|
| Scan protocol |
The microarray was processed using the Genepix pro v6.0 and scanned with a Axon Genepix4000B scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.5.1 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.
|
| |
|
| Submission date |
Feb 21, 2012 |
| Last update date |
Aug 18, 2012 |
| Contact name |
Hidehiro Kondo |
| E-mail(s) |
h-kondo@kaiyodai.ac.jp
|
| Phone |
81354630174
|
| Organization name |
Tokyo University of Marine Science and Technology
|
| Lab |
Laboratory of Genome Science
|
| Street address |
4-5-7 Konan, Minato
|
| City |
Tokyo |
| ZIP/Postal code |
1088477 |
| Country |
Japan |
| |
|
| Platform ID |
GPL15258 |
| Series (1) |
| GSE35966 |
Identification of differently expressed genes in Rainbow trout muscle under restricted feeding |
|
