Genomic DNA was prepared from whole blood collected in EDTA with a Puregene DNA isolation kit (Gentra Systems).
Label
biotin
Label protocol
According to manufacturer (Affymetrix).
Hybridization protocol
DNA was digested with HindIII or XbaI, ligated, PCR amplified, fragmented, end-labeled and hybridized to the chip according the the manufacturers instructions.
Scan protocol
The arrays were then washed using Affymetrix fluidics station 450 and scanned using the GeneChip Scanner 3000 7G Plus.
Description
data derived from two pools of 20 statin-tolerant controls
Data processing
SNP intensity signals were obtained using CEL files generated by Affymetrix GTYPE using the DM algorithm. A general linear regression model (Macgregor S, Visscher PM, Montgomery G, Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates. Nucleic Acids Res 2006; 34(7):e55) was used to identify differences between pools and calculate a z-score (the p-value of the z-test) for each SNP-pool comparison. The data table linked to GSE17574 contains the calculated z-score for each SNP comparing case pools to control pools.
