|
| Status |
Public on Oct 16, 2012 |
| Title |
66VO-I16 |
| Sample type |
RNA |
| |
|
| Source name |
intestine from early infected animal fed 66VO diet
|
| Organism |
Sparus aurata |
| Characteristics |
diet: vegetable oil
infection: intestinal parasite Enteromyxum leei
infective status: Early
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from intestine tissue was extracted with the ABI PRISM 6100 Nucleic Acid Prepstation
|
| Label |
Cy3
|
| Label protocol |
250 ng of total RNA was labeled using the Quick Amp Labeling Kit (Agilent) to produce Cyanine 3-CTP labeled cRNA.
|
| |
|
| Hybridization protocol |
Labelled cDNA samples were mixed with sheared salmon sperm genomic DNA as blocker. The cDNA mixture was concentrated by precipitation with 3M NaOAC (pH 5.5) and absolute ethanol at -20 oC for 30 minutes followed by centrifugation at 12500 x g for 30 minutes. Following removal of supernatant, the cDNA pellet was resuspended in 70 µl slide hyb buffer #1 (Ambion) and was then denatured at 95 oC for 2 minutes. The hybridisation mixture was then added to the microarray slide and sealed using a coverslip (Erie Scientific). Hybridisations were performed in a hybridisation chamber (Genetix) at 42 oC for 16 hours. Following hybridisation the slides were washed (2 x 5 minute washes using 0.2 X SSC/0.1 % SDS and 2 x 5 minute washes using 0.2 X SSC) using an Advawash automatic washing station (Advalytix).
|
| Scan protocol |
Agilent G2565BA Microarray Scanner
|
| Data processing |
Data were extracted using the Agilent Feature Extraction Software 9.5.3, 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 11.5.1 software (Agilent).
|
| |
|
| Submission date |
Feb 08, 2012 |
| Last update date |
Oct 16, 2012 |
| 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 |
GPL15203 |
| Series (1) |
| GSE35633 |
Effects of the nutritional background and parasite infection on the intestine transcriptome of gilthead sea bream, Sparus aurata |
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