|
| Status |
Public on Sep 03, 2010 |
| Title |
Mouse 147, gastrocnemius muscle, low fat diet, week 8 |
| Sample type |
RNA |
| |
|
| Source name |
mouse 147, gastrocnemius muscle, low fat diet, week 8
|
| Organism |
Mus musculus |
| Characteristics |
subject: mouse 147
tissue: gastrocnemius muscle
diet: low fat diet
strain: C56BL/6J
gender: Male
age: 20 weeks
|
| Treatment protocol |
After 8 weeks of diet intervention, mice were sacrificed, the gastrocnemius and quadriceps muscles were 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 randomly assigned to the LF or the HF group for 8 weeks
|
| 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 and FDR < 0.05
|
| |
|
| Submission date |
Sep 16, 2009 |
| Last update date |
Sep 03, 2010 |
| Contact name |
Janneke de Wilde |
| E-mail(s) |
j.dewilde@HB.unimaas.nl
|
| 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) |
| GSE18127 |
Hoxd genes and fiber type-specific markers specify adult mouse muscle type in a diet-independent way |
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