5 protocols
AccessionNameType
P-MTAB-27285
bioassay_data_transformation
Fluorescence intensities were normalized to the average fluorescence of the entire microarray. The detailed protocol for further processing of the arrays is available from Affymetrix.
P-MTAB-27284
feature_extraction
After washing and staining, the fluorescence intensity was measured twice for each array using the GeneArray scanner (Affymetrix).
P-MTAB-27282
hybridization
The generated biotin-labeled cRNA was fragmented by metal-induced hydrolysis, and was hybridized to the GeneChip array (HG-U133A, Affymetrix). The detailed protocol for hybridization, washing and staining of the arrays is available from Affymetrix. Microarray gene expression analysis was performed in triplicates as previously described (Oswald et al., 2006).
P-MTAB-27283
nucleic_acid_extraction
High-quality RNA was isolated with the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions.
P-MTAB-27286
labeling
5 ?g of total RNA were used per patient sample for first strand cDNA synthesis, according to the Eukaryotic Target Labeling protocol as recommended by the manufacturer. Synthesis of biotin-marked cRNA was performed as described in the in vitro-transcription protocol (Affymetrix, Santa Clara, CA, USA).