|
| Status |
Public on May 13, 2008 |
| Title |
SI3_wk4_LF |
| Sample type |
RNA |
| |
|
| Source name |
SI3 after 4 wks on a LF diet
|
| Organism |
Mus musculus |
| Characteristics |
C57Bl/6J male mice, 9wks old at start of diet intervention
|
| Treatment protocol |
After a run-in period of 3 weeks on a low-fat diet, 9 weeks old mice were fed a high- (HF) or a low-fat (LF) purified diet for 2, 4, and 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 and per time point (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 400.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip Scanner 3000
|
| Description |
pooled total RNA sample of 6 mice
|
| Data processing |
Data analysis was performed using Microarray Analysis Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 500.
|
| |
|
| Submission date |
Jul 25, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| 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) |
| GSE8582 |
Role of small intestine in the development of dietary fat-induced obesity and insulin resistance in C57BL/6J mice. |
|
| Relations |
| Reanalyzed by |
GSE119085 |
