RNA was isolated using TRIzol (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit with on-column DNAse treatment (Venlo, the Netherlands). RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.
Label
biotin
Label protocol
Synthesis of cDNA, cRNA amplification, and hybridization of cRNA onto the Illumina Human-6 v2.0 Expression BeadChips (San Diego, CA, USA) were performed as per manufacturer's instructions.
Hybridization protocol
Synthesis of cDNA, cRNA amplification, and hybridization of cRNA onto the Illumina Human-6 v2.0 Expression BeadChips (San Diego, CA, USA) were performed as per manufacturer's instructions.
Scan protocol
The slides were scanned on a BeadArray Reader (Illumina, Inc.).
Description
The cell lines were maintained in RPMI 1640 (Invitrogen, Carsbad, CA, USA) supplemented with 10% fetal calf serum, 2 mM L-glutamine (Invitrogen) and 1% Penicillin/Streptomycin (Invitrogen) under standard conditions.
Data processing
The data was extracted and quality controlled using the Gene Expression module v3.1.7 of Illumina´s BeadStudio software (v3.1.0.0). Variance-stabilizing transformation (Lin et al., 2008) and quantile normalization on the probe level was carried out using the statistical package R and the Bioconductor package lumi (Du et al., 2008; Gentleman et al., 2004).
