|
| Status |
Public on Jan 05, 2012 |
| Title |
headkidney_lineR3_day0_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Head kidney from non-infected carps (CyHV-3) at day 0.
|
| Organism |
Cyprinus carpio |
| Characteristics |
line: R3
weight: around 120gr
tissue: Head kidney
|
| Biomaterial provider |
Common carp used in this study were obtained and bred at the Institute of Ichthyobiology & Aquaculture, Polish Academy of Sciences, ul. Kalinowa 2, 43-520 Chybie, Poland
|
| Treatment protocol |
Before sampling, fish were anaesthetised by the use of Propiscin (5ml/L).
|
| Growth protocol |
Fish from each group were grown in aquaria with UV treated recirculating water and bio-filters. The total capacity of the system was 3 m3 and the water temperature was maintained at 21±1°C. Daily feeding with commercial carp pellets (Aller Aqua, Poland) was applied at 5-3% body weight per day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated from head kidney samples using the RNeasy Mini Kit (Qiagen, Japan) according to the manufacturer’s instruction.
|
| Label |
Cy3
|
| Label protocol |
Labelling was performed using Cy3 dye according to the Low Input Quick Amp Labeling Kit Protocol (Agilent Technologies, USA).
|
| |
|
| Hybridization protocol |
Hybridization was carried out for 17 h at 65°C. After 17 h, the glass slides were washed with GE Wash Buffer for 1 min at RT and subsequently with GE Wash Buffer 2 for 1 min at 37°C using the Low Input Quick Amp Labeling Kit (Agilent Technologies, USA).
|
| Scan protocol |
After washing the glass slides were dried and scanned immediately using the Gene Pix 4000B scanner (Axon Instruments, USA) and the Gene Prix Pro 6.1 software. The data was extracted using the Agilent Feature Extraction software.
|
| Data processing |
The data was analyzed in R using the 'limma' package from the Bioconductor project. The single-channel arrays were first background corrected with the normexp method and an offset of 50 and then normalized with a quantile normalization.
|
| |
|
| Submission date |
Jul 06, 2011 |
| Last update date |
Jan 05, 2012 |
| Contact name |
Leonor Palmeira |
| Organization name |
University of Liege
|
| Department |
Faculty of Veterinary Medicine
|
| Lab |
Immunology-Vaccinology
|
| Street address |
Bd Colonster 20
|
| City |
Liege |
| ZIP/Postal code |
4000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13819 |
| Series (1) |
| GSE30426 |
Transcriptional analysis of common carp (Cyprinus carpio L.) immune response against Cyprinid herpesvirus 3 (CyHV-3). |
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