|
| Status |
Public on Dec 01, 2010 |
| Title |
1536LD |
| Sample type |
RNA |
| |
|
| Source name |
longissimus thoracis et lumborum muscle from 190-days-old pigs
|
| Organism |
Sus scrofa |
| Characteristics |
group: HIGH_fattening
tissue: longissimus thoracis et lumborum muscle
age: 190 days-old
breed: Duroc
|
| Treatment protocol |
After slaughter, controled animals (n=350) were ranked based in 13 carcass, plasma and muscle fat deposition and fat composition traits. The top and bottom extreme of this distribution were selected to form the HIGH (n=10) and LOW (n=9) groups for longissimus thoracis et lumborum muscle microarrays experiment
|
| Growth protocol |
Duroc pigs were grown in standard commercial conditions, fed a commercial pellet diet and slaughtered at 190 days of age. 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 thoracis et lumborum muscle using Ribopure kit (AMBION) 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 |
Duroc commercial line
|
| 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.
|
| |
|
| Submission date |
Nov 30, 2010 |
| Last update date |
Dec 08, 2010 |
| Contact name |
angela canovas |
| E-mail(s) |
angela.canovas@irta.cat
|
| Organization name |
irta
|
| Street address |
191, rovira roure
|
| City |
lleida |
| State/province |
lleida |
| ZIP/Postal code |
25198 |
| Country |
Spain |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE25708 |
Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects |
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