6 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = RMA-normalized signal intensity
image_aquisition
GeneChips were scanned using the GeneChip Scanner 3000 7G.
feature_extraction
Expression levels of 17,527 genes were extracted from Affymetrix HU133 Plus 2.0 arrays using updated array annotation (Dai et al., 2005) based on reorganizing probes to gene specific probe sets, excluding inaccurate or wrongly annotated probes.
hybridization
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
labeling
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
nucleic_acid_extraction
Trizol extraction of total RNA was performed according to the manufacturer's instructions.