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Sample GSM908348 Query DataSets for GSM908348
Status Public on Aug 22, 2012
Title colon_WT_control_repl1
Sample type RNA
Source name colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 1
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
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

Data table header descriptions
VALUE RMA signal (as log2)

Data table
10338001 11.53400968
10338002 4.473729368
10338003 9.839170753
10338004 9.169373743
10338005 2.128958849
10338006 2.444527903
10338007 2.630754229
10338008 2.951938473
10338009 6.672375497
10338010 2.170843245
10338011 4.072001209
10338012 2.246334458
10338013 1.951352538
10338014 2.043685899
10338015 1.956604511
10338016 5.425544818
10338017 12.98993653
10338018 4.904244506
10338019 3.63280849
10338020 6.426437835

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.

Supplementary file Size Download File type/resource
GSM908348_G024_A07_02_14A_C_WT_CTRL.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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