|
| Status |
Public on Jun 18, 2012 |
| Title |
SI3, 2 wks on a HF-SO diet |
| Sample type |
RNA |
| |
|
| Source name |
SI3 after 2 wks on a HF-SO diet
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 3
dietary fat type: safflower oil
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
| Treatment protocol |
Nine-week-old C57Bl/6J mice were fed a low-fat diet (LF-PO) and three different types of high-fat diet, based on palm oil (HF-PO; P/S1.0), olive oil (HF-OO; P/S4.6) and safflower oil (HF-SO; P/S10.1) for 8 weeks.
|
| Growth protocol |
Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group (n=6).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Pooled total RNA sample of 6 mice.
SI3_wk2_HF-SO
|
| Data processing |
Data analysis was performed in Bioconductor using the MAS5 algorithm. The mean target intensity of each array was set to 100.
|
| |
|
| Submission date |
Oct 15, 2009 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE18586 |
Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine |
|
