6 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = RMA-calculated signal intensity
image_aquisition
Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)
feature_extraction
Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.
hybridization
Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual)
labeling
Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)
nucleic_acid_extraction
TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers’ protocols