|
| Status |
Public on Oct 31, 2017 |
| Title |
0600-4 |
| Sample type |
RNA |
| |
|
| Source name |
Whole 30-day larva, 21h Zeitgeber time
|
| Organism |
Sparus aurata |
| Characteristics |
age: Whole 30-day larva
zeitgeber time (hrs): 21:00
|
| Growth protocol |
Gilthead sea bream larvae were reared in four circular 250 L tanks under constant temperature (19 °C), salinity (34 ‰) and 12 h light : 12 h darkness cycle. The larvae were fed ad libitum with rotifers (Brachionus rotundiformis Bs-strain and B. plicatilis S-1-strain) supplied at a density of 10 rotifers/mL and enriched with the microalgae Nannocholopsis gaditana, from day 4 post-hatching (dph) and subsequently with Artemia sp. nauplii from 18 dph until the end of experiment. Larvae were sampled at 30 dph during a 24 h cycle taking 10 individuals every 3 hours (00:00, 03:00, 06:00, 09:00, 12:00, 15:00, 18:00, 21:00 and 24:00 h Zeitgeber time) and preserving them in RNAlater.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole larvae using an Ultra-Turrax T8 and the NucleoSpin RNA II kit, including the on column RNase-free DNase digestion included with the kit. RNA quantity was measured spectrophotometrically at 260 nm with the BioPhotometer Plus giving a yield between 3 and 15 µg
|
| Label |
Cy3
|
| Label protocol |
Total RNA (150 ng) from individual fish (n=6 for each group) were labelled with cyanine 3-CTP (Low Input Quick Amp Labelling Kit, Agilent)
|
| |
|
| Hybridization protocol |
Each sample (600ng) was hybridized to the Custom Sea bream Oligo Microarray Kit (Agilent p/n 067581) at 65 ºC for 17 h using Agilent GE hybridization kit
|
| Scan protocol |
Arrays were scanned with Agilent scanner G2565C
|
| Description |
0600-4.txt
|
| Data processing |
Spot intensities and other quality control features were extracted with Agilent Feature Extraction software version 11.5.1.1, and was further analyzed, including percentile shift normalization, one-way ANOVA, principal components analysis and k-means clustering of differentially expressed genes, by means of GeneSpring GX 13.0 software (Agilent)
|
| |
|
| Submission date |
Dec 23, 2014 |
| Last update date |
Oct 31, 2017 |
| Contact name |
Josep A Calduch-Giner |
| E-mail(s) |
j.calduch@csic.es
|
| Phone |
0034964319500
|
| Organization name |
Institute of Aquaculture Torre de la Sal (CSIC)
|
| Street address |
Ribera de Cabanes
|
| City |
Castellón |
| ZIP/Postal code |
12595 |
| Country |
Spain |
| |
|
| Platform ID |
GPL19579 |
| Series (1) |
| GSE64481 |
Circadian rythms of gene expression in a continuosly growing fish larva |
|
