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| Status |
Public on Aug 03, 2015 |
| Title |
colon_control_with Abx_repl3 |
| Sample type |
RNA |
| |
|
| Source name |
colon of mouse, after 14 days on a Westernized high fat (control) diet and Abx, replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
backgroud: C57BL/6J
gender: male
age: 11 weeks
tissue: colon
diet: 14 days on a Westernized high fat (control) diet and Abx
|
| Treatment protocol |
Mice were fed a Westernized high fat control diet, or the same diet supplemented with 0.5 µmol heme/g diet. One group of control and one group of heme mice received a mixture of broad spectrum Antibiotics (Abx) (ampicilin, neomycin and metronidazole) in their drinking water. After 14 days of intervention, mice were killed and the colon was taken out. Mesenteric fat was removed from the colon. Colons were cut open longitudinally, washed in PBS, and scraped. RNA was isolated from scrapings and analysed by microarray.
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| 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).
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| |
|
| 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.
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| 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).
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| |
|
| Submission date |
Sep 06, 2012 |
| Last update date |
Aug 03, 2015 |
| 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 |
GPL11533 |
| Series (1) |
| GSE40670 |
Microbiota facilitates dietary heme-induced epithelial hyperproliferation and hyperplasia by breaking the mucus barrier |
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