Twenty-eight Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), DIM (153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to treatment groups based to one of the four dietary treatments. The dietary treatments were a basal diet supplemented with either: 2.7% rapeseed oil as a source of cis-9-18:1 (oleic acid), 2.7% soybean oil as a source of cis-9, cis-12-18:2 (linoleic acid), 2.7% linseed oil as a source of ALA or 2.7% of a 1:1:1 mixture of the three oils. The oil supplements were included in the concentrate, which was fed, together with corn silage and grass silage, as a total mixed ration (TMR; Table 1). Corn silage, grass silage and concentrates comprised 52, 12 and 36% of the total TMR, respectively, on a DM basis. The cows were grazing on pasture composed of ryegrass (Lolium perenne L.), with approximately 20% white clover (Trifolium repens L.), during the day (from 8:00h until 16:00h) and were fed the TMR, indoors at night. The paddock was 5 ha in size and the stocking density was 16 cows/ha. Cows grazed the paddocks at an herbage allowance of approximately 5.5 kg of DM/cow per day, and were fed the TMR at a level of about 14.5 kg of DM/cow per day. After the first period of 23 days (Experimental period I, final DIM = 176 ± 32.8 days), all cows were switched to a control diet without oil supplementation for an additional 28 days (Experimental period II; final DIM= 204 ± 32.8 days).
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Santa Clara, CA, Affymetrix).
Hybridization protocol
Following fragmentation, cRNA were hybridized for 16 hr at 45C with constant rotational mixing at 60 rpm on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using an Affymetrix GeneGhip Scanner 7G and Affymetrix GeneChip Operating Software version 1.4
Description
080312MJA_bovine_100180-42.CEL
Data processing
All microarray analysis including preprocessing, normalization and statistical analysis was carried out using R Software (version 2.10 and Bioconductor version 2.5). Data were quality assessed before and after normalization using a number of built-in quality control methods implemented in the Bioconductor affycoretools and associated packages to identify eventual irregularities of array hybridization, RNA degradation, and data normalization. Expression levels of probe sets were summarized using the library GC content-corrected robust multichip average algorithm (GC-RMA; (Wu et al., 2004), employing the empirical Bayes approach for background correction followed by quantile normalization.
