breed: LD/LW x Duroc selection: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits age: 170 days-old tissue: Longissimus Dorsi muscle
Treatment protocol
After slaughter, controled animals were ranked based in 33 composition, conformation and meat quality and compositional traits.
Growth protocol
A total of 75 animals from a LD/LW x Duroc cross were raised together in an experimental farm. 60 piglets were selected randomly after the postweaning period. During the feeding period, they were feed ad libitum. One piglet died during this time and was excluded from further studies. Tissue samples were collected at slaughter, snap froxen in LN2 and stored at -80ºC until analysis
Extracted molecule
total RNA
Extraction protocol
total RNA was extracted from longissimus dorsi muscle using RNeasy Protect Mini kit (QIAGEN, Hamburg, Germany) following the manufacturer's protocol
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
Hybridisation protocol as recommented by Affymetrix using the Porcine Genome Array from Affymetrix.
Scan protocol
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A, as recommended by Affymetrix
Description
LD/LW x Duroc pigs cross
Data processing
Data pre-processing, normalisation and class comparison analysis were carried out with the BRB-ArrayTools software version 3.7.1, which is available online at http://linus.nci.nih.gov/BRB-ArrayTools.html, as follows: microarray data normalisation was performed using the gcRMA algorithm, which corrects the intensity of each probe by its GC content; genes showing minimal variation across the set of arrays were excluded from the analysis, that is, only genes whose expression differed above 1.5 fold from the median in at least 20% of the arrays were retained. From the total 23937 spots of the array, 4299 spots passed these filtering conditions. For each probe, expression fold-change was calculated as the ratio between median values in both groups.
