|
| Status |
Public on Jan 01, 2014 |
| Title |
SCAT_RFIpl_20kg_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
SCAT, high-RFI, 20kg body weight
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: SCAT
strain: RFIpl
feed condition: Ad libitum
|
| Growth protocol |
The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA extraction, samples of frozen tissues (80 to 100 mg each) were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a TissueLyser (Qiagen) and were then treated as previously described (Vincent et al., 2012). RNA was finally purified using a silica-membrane technology under vacuum (Nucleospin 8 RNA kit, Macherey Nagel, Hoerdt, France)
|
| Label |
Cy3
|
| Label protocol |
Total RNA (150 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)
|
| |
|
| Hybridization protocol |
Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 1.65 µg of Cy3-labeled cRNA sample per hybridization. Hybridization reactions were performed at 65°C for 17 h using Agilent’s Gene Expression Hybridization Kit
|
| Scan protocol |
After washing, microarrays were scanned at 5 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505C, and images were analyzed with Agilent Feature Extraction Software (Version 10.7.3.1, protocol GE1_107_Sep09)
|
| Description |
Gene expression in 20 kg body weight pig subcutaneous adipose tissue with high residual feed intake
|
| Data processing |
All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg).
|
| |
|
| Submission date |
Jun 10, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Annie Vincent |
| E-mail(s) |
annie.vincent@inra.fr
|
| Organization name |
INRA
|
| Lab |
UMR PEGASE
|
| Street address |
domaine de la prise
|
| City |
Saint-Gilles |
| ZIP/Postal code |
35590 |
| Country |
France |
| |
|
| Platform ID |
GPL15007 |
| Series (1) |
| GSE47770 |
Effect of selection on residual feed intake on gene expression in porcine subcutaneous adipose tissue (20 kg body weight) |
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