RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control (RIN>8) was performed with Agilent Bioanalyser.
Label
biotin
Label protocol
biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit from Applied Biosystems
Hybridization protocol
Standard Illumina hybridization protocol
Scan protocol
Standard Illumina scanning protocol
Description
replicate 1
Data processing
Data was processed using R2.11.1, beadarray 1.16.0. Differential expression was analysed with limma using design matrix design=cbind(M.WT=c(1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0), M.MD=c(0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0), F.WT=c(0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0), F.MD=c(0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1), Array2=c(0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1))
