|
| Status |
Public on Aug 22, 2012 |
| Title |
colon_WT_control_repl3 |
| Sample type |
RNA |
| |
|
| Source name |
colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129S1/SvImJ
genotype/variation: wild type
gender: male
age: 7-9 weeks
tissue: colon
diet: control
|
| Treatment protocol |
Seven to nine week-old mice were placed on a Westernized high fat diet diet (40 energy% fat [mainly palm oil and corn oil] and low in calcium [30 µmol/g]), or the same diet supplemented with 0.5 µmol heme/g diet. After 14 days of intervention, mice were killed and colon was removed.
|
| Growth protocol |
Wildtype (129S1/SvImJ) and PPARα knockout (129S4/SvJae-Pparatm1Gonz/J) mice were purchased from The Jackson Laboratory and bred in our facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from colon using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked by 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 |
The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).
|
| |
|
| Hybridization protocol |
The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 23 arrays that were used in this experiment were provided as subset of a 1x 24 array plate. Array hybridization, washing and scanning 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' (v1.18.1).
|
| |
|
| Submission date |
Apr 03, 2012 |
| Last update date |
Aug 22, 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 |
GPL11533 |
| Series (1) |
| GSE37006 |
Dietary heme mediated PPARα activation does not affect the heme-induced epithelial hyperproliferation and hyperplasia in mouse colon |
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