Charles River Breeding Laboratory, Someren, The Netherlands
Treatment protocol
During section, the distal colon was rinsed with 70% ethanol at 4°C, subsequently scraped with sterilized glass slides and fixed in RNAlater® (Ambion®, Cambridgeshire, U.K.) according to the manufacturer’s protocol.
Growth protocol
Rats were fed either 10 g quercetin/kg diet or the control diet(RM3 [E] FG SQC rat breeder diet obtained from SDS Special Diets Services, Witham, England) for 11 weeks.
Extracted molecule
total RNA
Extraction protocol
RNA extraction was performed with the TRIzol Reagent (Life Technologies, Paisley, U.K.), as described by the manufacturer. Total RNA was purified with the NucleoSpin® RNA II kit (Machery-Nagel, Düren, Germany), including a DNAse incubation step to digest possible traces of DNA. Subsequent analysis on the Agilent 2100 bioanalyser (Agilent Technologies, Palo Alto, California, U.S.A.) indicated high quality total RNA (28S/18S ribosomal RNA ratios ~2.0) that was suitable for hybridization
Label
Biotin
Label protocol
For RNA labeling, GeneChip® One-Cycle Eukaryotic Target Labeling Assay for expression analysis was performed, as described in the Affymetrix® GeneChip® Expression Analysis Technical Manual
Hybridization protocol
Hybridisation on Affymetrix® GeneChip® arrays was processed according to the GeneChip® One-Cycle Eukaryotic Target Labeling Assay.
Scan protocol
Affymetrix® GeneChip® arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix® Inc., Santa Clara, California, U.S.A.).
Description
Control, sample 2
Data processing
Data were processed with MAS 5.0 and a scaling factor of 200 was applied.
