RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified. RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).
Label
biotin
Label protocol
Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).
Hybridization protocol
Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.
Scan protocol
Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.
Data processing
Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method. Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA). Expression values were normalized using quantile normalization with default settings.
