6 protocols
normalization data transformation protocol
The data were analyzed with Partek Genomics Suite version 6.6. Normalization was performed using RMA background correction with pre-background adjustment for GC content. Exons were summarized to genes using average method. Only probes with a log2 intensity greater than 5.6 in at least 10% of all samples were kept for further analysis. ID_REF = VALUE = log2 RMA
array scanning protocol
GeneChip were scanned by Affymetrix® GeneTitan.
hybridization protocol
Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hours at 45°C on Human Gene 1.1ST array plates. GeneChips were washed and stained in the Affymetrix® GeneTitan device.
labelling protocol
100ng of total RNA was amplified by the Ambion® WT expression kit (ref 4411974) to generate cDNA sense target. Then products were labeled (biotinylated) using Affymetrix WT terminal labelling kit (ref 901524)
nucleic acid extraction protocol
Qiazol extraction followed Qiagen miRNeasy protocol
sample treatment protocol
All patients received epirubicin (75 mg/m2)-cyclophosphamide (750 mg/m2) intravenously every 3 weeks for four cycles followed by docetaxel (100 mg/m2) every 3 weeks for four cycles. We selected only patients with complete therapeutic response.