6 protocols
AccessionType
hybridization protocol
Affymetrix Generic Hybridization
nucleic acid labeling protocol
Labeling of samples was carried out according to the manufacturer’s standard protocol
bioassay_data_transformation
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.
image_acquisition
Standard Affymetrix protocol scanning biotin labeled GeneChips
(Parameters: Scanning hardware = GeneChip Scanner 3000 [Affymetrix], Scanning software = MAS/GCOS/GREX [Affymetrix])
specified_biomaterial_action
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).
nucleic_acid_extraction
RNeasy Lipid Tissue Midi Kit (Qiagen UK)
(Parameters: Extracted product = total_RNA, Amplification = none)