normalization data transformation protocol
Bead-level data were obtained using GenomeStudio (Gene expression Version 1.7.0). Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed ID_REF = VALUE = Quantile-normalized and log2-transformed signal
array scanning protocol
The chips were scanned by Illumina iScan system.
1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.
500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)
nucleic acid extraction protocol
RNA was isolated using RNeasy mini kit (QIAGEN, Valencia, CA) and quality was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
Cells were grown in adherent conditions and cell pellets were harvested when cells were ~70% confluent.