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These are the processed data files related to the bulk expression data from breast tumors treated on the TRIO B07 trial (NCT00769470). Tumor or tumor bed tissue was collected and subjected to the Agilent Whole Human Genome 44K 2-color chip pre-treatment, on-treatment (after 1 cycle of HER2-targeted therapy alone, either trastuzumab, lapatinib, or the combination), and post-treatment (at definitive surgery after 6 cycles of docetaxel/carboplatin in combination with assigned HER2-targeted therapy). The raw data is available at GEO (GSE130788). The folder also includes the full protocol for the TRIO B07 trial and the gene sets assessed.