e pens of each group were fed one of two experimental diets containing 25 32% fish meal, 40 45% plant meals and 27. 5 30% oil supplied either as standard northern FO or as a VO blend comprising rapeseed, palm and Camelina oils in a ratio of 5,3,2. Diets were formulated to fully satisfy the nutritional requirements of salmonid fish and con tained similar levels of PUFA but different n 3 and n 6 PUFA contents, 25. 3% and 4. 6% in the FO diet and 13. 4% and 17. 1% in the VO diet, respectively. After 55 weeks, 25 fish per pen were sampled 24 h after the last meal. Fish were killed by a blow to the head follow ing anaesthesia, and intestinal tissue col lected, immediately frozen in liquid nitrogen and stored at ?70 C prior to analyses. Further details can be found in Bell et al.
Lipid extraction and fatty acid analyses Total lipid from 1 g of intestine of four fish per treat ment was extracted and determined gravimetrically, and fatty acid methyl esters prepared by acid catalysed transesterification of total lipid. FAME were separated and quantified by gas chromatography AV-951 as described in detail previously. Significant differences in intestinal fatty acid composition were determined by two way ANOVA using the SPSS 16. 0 statistical package. RNA extraction and purification Intestinal tissue from six individuals per experi mental group was homogenised in 2mL TRI Reagent and total RNA isolated following manufacturers instruc tions. RNA quantity and quality were assessed by gel electrophoresis and spectrophotometry, and 100 ug of total RNA from each sample fur ther cleaned by mini spin column purification.
Microarray hybridizations, image processing and statistical analysis The TRAITS SGP salmon 17k cDNA microarray described by Taggart et al. was used. A dual labelled experimental design was employed, with each sample being competi tively hybridised against a common pooled reference. The experiment comprised 2 genotypes �� 2 diets �� 6 biological replicates. Indirect labelling was employed for preparing the microarray targets. Antisense amplified RNA was produced from 500 ng of purified total RNA per sample using the Amino Allyl MessageAmpTM II aRNA Amplification Kit as per manufacturers instructions, followed by Cy3 or Cy5 fluor incorporation through dye coupling reaction. Microarray hybridizations were performed in a Lucidea semi automated system with out pre hybridization.
For each array, every labelled bio logical replicate and corresponding pooled reference were combined and added to the hybridization solution. Two post hybridization automatic washes followed by six manual washes to a final stringency of 0. 1�� SSC were performed before scanning. Scanning was performed at 10 um resolution using an Axon GenePix 4200AL Scanner. Laser power was constant and auto PMT was enabled to adjust each channel at less than 0. 1% feature saturation and Cy3 Cy5 mean intensity close to one. BlueFuse software was used to identify fea tures and extract fluorescence intensi