|
| Status |
Public on Dec 19, 2012 |
| Title |
colon control repl3 |
| Sample type |
RNA |
| |
|
| Source name |
colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
backgroud: C57BL/6J
gender: male
age: 11 weeks
tissue: colon
diet: Westernized high fat (control) diet
|
| Treatment protocol |
Male control and heme-fed mice were maintained on a high fat-low calcium diet (with or without heme) for 2 weeks. After 2 weeks diet intervention all mice were sacrificed and colons were taken out. Mesenteric fat was removed. Colons were cut open longitudinally, washed in PBS, and epithelial cells were scraped off.
|
| Growth protocol |
C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from colonic scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
|
| Label |
biotin
|
| Label protocol |
One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
|
| |
|
| Hybridization protocol |
Hybridization, washing and scanning of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument.
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).
|
| |
|
| Submission date |
Sep 06, 2012 |
| Last update date |
Dec 19, 2012 |
| 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 |
GPL11533 |
| Series (1) |
| GSE40672 |
Dietary heme alters microbiota and mucosa of mouse colon without functional changes in host-microbe cross-talk. |
|
