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Sample GSM908370 Query DataSets for GSM908370
Status Public on Aug 22, 2012
Title colon_PPARa-/-_heme_repl6
Sample type RNA
Source name colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 6
Organism Mus musculus
Characteristics strain: 129S4/SvJae-Pparatm1Gonz/J
genotype/variation: PPARa knockout
gender: male
age: 7-9 weeks
tissue: colon
diet: heme
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 11.51828709
10338002 4.550986304
10338003 9.903070964
10338004 9.222009041
10338005 2.213105435
10338006 2.489303257
10338007 2.680250267
10338008 3.039042182
10338009 6.851680605
10338010 2.232693092
10338011 4.199643012
10338012 2.340941044
10338013 2.023038643
10338014 2.117503814
10338015 2.046179931
10338016 5.597903847
10338017 12.86012188
10338018 4.990932763
10338019 3.646205046
10338020 6.613331214

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.

Supplementary file Size Download File type/resource
GSM908370_G024_H09_24_42B_C_KO_HEME.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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