Affymetrix Generic Hybridization
nucleic acid labeling protocol
Labeling of samples was carried out according to the manufacturer’s standard protocol
Affymetrix CEL files loaded into Bioconductor and normalised with the rma function in the Affy package: rma(myaffybatch, normalize=TRUE,background=TRUE,bgversion=2). Values are antilogs (base 2) of calculated log values and correspond to linear scale.
Standard Affymetrix protocol scanning biotin labeled GeneChips
(Parameters: Scanning hardware = GeneChip Scanner 3000 [Affymetrix], Scanning software = MAS/GCOS/GREX [Affymetrix])
Diabetes was induced by a single tail vein injection of streptozotocin (20mg/kg in citrate buffer, pH 4.0) following which all rats became diabetic (blood glucose >15mM after 3 days). Two weeks after administration of streptozotocin, hypertension was induced by dietary supplementation of Indole-3-carbinol (0.125% by mass).
RNeasy Lipid Tissue Midi Kit (Qiagen UK)
(Parameters: Extracted product = total_RNA, Amplification = none)