|
| Status |
Public on Aug 10, 2010 |
| Title |
muscle_HF_ d56_biorep3 |
| Sample type |
RNA |
| |
|
| Source name |
mouse 144, quadriceps muscle, high fat diet, day 56
|
| Organism |
Mus musculus |
| Characteristics |
protocol: high fat diet
time: day 56
tissue: quadriceps muscle
strain: C56BL/6J
gender: Male
age: 20 weeks
|
| Treatment protocol |
After 0 days or 56 days of diet intervention, mice were sacrificed, the quadriceps muscle was dissected and snap-frozen in liquid nitrogen
|
| Growth protocol |
Mice were fed a standard growth diet for 3 weeks prior to switching to the LF run-in diet for 3 weeks. Following the run-in period mice were sacrificed or randomly assigned to the LF or the HF group for 56 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
According the manufactures instruction, total RNA was extracted from the quadriceps muscle with Trizol reagent (Invitrogen, Breda, the Netherlands) and purified with the Rneasy Mini Kit
(Qiagen, Venlo, the Netherlands). Contaminating genomic DNA was removed with the RNase-free DNase set (Qiagen, Venlo, the Netherlands) according the manufactures instructions.
|
| Label |
biotin
|
| Label protocol |
Labeling was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)
|
| Scan protocol |
Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)
|
| Description |
Before the diet intervention mice (age: 9 weeks) were switched to the LF run-in diet for 3 weeks
|
| Data processing |
Expression levels of probe sets were normalized using GC-RMA(slow) (unlogged scale). Probe sets were redefined according to Dai et al (Nucleic Acids Research, 2005). In this method probes are annotated
using up to date databases and assigned to unique gene identifiers, in this case Entrez ID's, instead of the classic GeneChip probe sets. As selection criteria we used: fold change > 1.3 a p value < 0.05 and FDR < 0.05
|
| |
|
| Submission date |
Aug 10, 2009 |
| Last update date |
Aug 10, 2009 |
| Contact name |
Janneke de Wilde |
| E-mail(s) |
[email protected]
|
| Phone |
+31 433 881 509
|
| Fax |
+31 43 367 09 76
|
| Organization name |
Maastricht University
|
| Department |
Human Biology
|
| Street address |
Universiteitssingel 50
|
| City |
Maastricht |
| ZIP/Postal code |
6229 ER |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL7546 |
| Series (1) |
| GSE17576 |
A high fat diet causes obesity and insulin resistance in mice, but induces small changes in the muscle transcriptome |
|
