Sex: male mouseid: 372 diet_group: standard, low fat diet (formulation according to Research Diets Inc.: D12450B) tissue: proximal colon genotype: wildtype strain: Balb/c
Treatment protocol
Mice did not receive any specific treatment
Growth protocol
Male and female wild-type B6 and BALB/c mice were purchased from Harlan (Harlan, Horst, the Netherlands) at an age of eight weeks. Mice were co-housed (five mice per cage) in isolated ventilated cages to limit environmental influences. The animals had free access to food (low fat diet, according to D12450B diet formulation, prepared by Research Diets Services, Wijk bij Duurstede, the Netherlands) and water. Between an age of 3 and 5 months all mice were sacrificed by cervical dislocation under anesthesia (isoflurane and oxygen). Subsequently approximately 1 cm of the proximal colon was removed for microarray analysis. All female mice were sacrificed during the diestrus phase of their ovarian cycle to ensure low stable levels progesterone and estrogens.
Extracted molecule
total RNA
Extraction protocol
RNA was purified using TRIzol (Life Technologies, Calsbad, CA, USA) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). 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
Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
Hybridization protocol
Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).
Scan protocol
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).
Data processing
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).
