array scanning protocol
BeadChips were dried and scanned with an Illumina Bead Array Reader (Illumina) confocal scanner, according to the manufacturer's instructions.
nucleic acid hybridization to array protocol
For each sample, 750ug of cRNA were hybridised for 18h at 55C to Human HT-12_V3_0_R1 Expression BeadChips (Illumina, San Diego, CA).
For each sample, 500 ng of total RNA were used to synthesize biotinylated cRNA with the Illumina RNA Amplification Kit (Ambion, Austin, TX). Synthesis was carried out according to the manufacturers instructions.
LOUCY cells were resuspended in Opti-MEM (Gibco) and electroporated in 4 mm cuvettes (300 V, 1000 F; Genepulser XCell, Bio-Rad) using Stealth siRNAs (Ambion) against CUX1 or negative control duplexes. Cells were rested for 15 min following electroporation before dilution into normal RPMI 10 percent FBS growth media.
nucleic acid extraction protocol
RNA prepared from cells 48-72 h later using an RNeasy mini kit (Qiagen) was used for cDNA preparation for microarrays according to manufacturers instructions (Illumina).