normalization data transformation protocol
The data were analyzed with GCRMA (Bioconductor) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. ID_REF = VALUE = GCRMA Signal Intensity (log2)
array scanning protocol
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133Plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
HeLa cells were nucleofacted with respective siRNAs and RNA was isolated after 72 hours
nucleic acid extraction protocol
RNA was extracted using RNA easy mini kit Cat:74104
sample treatment protocol
No treatment other then nucleofaction