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Table 1 Antibodies and probes used

From: Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression

Immunohistochemistry Manufacturer, clone Antigen retrieval Dilution Evaluation
Estrogen receptor alpha Lab Vision, SP1 0.01 M citrate NaOH, pH 6.0 1:4,000 Threshold at 5% positive nuclei
Estrogen receptor beta Novocastra, EMR02 0.001 M EDTA-NaOH, pH 8.0 1:100 Threshold at 5% positive nuclei
Progesterone receptor Lab Vision, SP2 0.01 M citrate NaOH, pH 6.0 1:2,000 Threshold at 5% positive nuclei
HER2/neu immunohistochemistry Dako, polyclonal 0.01 M citrate NaOH, pH 6.0 1:200 0 - 1 + -2 + 3 + according to DAKO manual
Cytokeratin 5/6 Dako, D5/6 B4 0.001 M EDTA-NaOH, pH 8.0 1:200 Threshold at 1% positive tumor cells
Cytokeratin 14 Novocastra, LL002 0.01 M citrate NaOH, pH 6.0 1:200 Threshold at 1% positive tumor cells
Cyclin D1 immunohistochemistry Lab Vision, SP4 0.001 M EDTA-NaOH, pH 8.0 1:800 Threshold at 5% positive nuclei
Mucin 1 Novocastra, MA695 0.001 M EDTA-NaOH, pH 8.0 1:800 0 negative; 1, 1% to 50%; 2, >50% tumor cells positive
Gross cystic fluid protein Novocastra, 23A3 0.001 M EDTA-NaOH, pH 8.0 1:800 Threshold at 1% positive tumor cells
In situ hybridization Probe Protocol Evaluation  
HER2/neu amplification Abbott PathVysion HER2 DNA Probe Kit Manufacturer's instructions Locus-specific signal to centromere signal ratio >2.0 considered amplified  
Cyclin D1 amplification Abbott Vysis LSI Cyclin D1/CEP11 Manufacturer's instructions Locus-specific signal to centromere signal ratio >2.0 considered amplified  
  1. EDTA, ethylenediamine tetraacetic acid. Lab Vision (Thermo Fisher Scientific, Fremont CA, USA); Novocastra (Leica Microsystems, Wetzlar, Germany); Dako (Glostrup, Denmark); Abbott (Abbott Park, IL, USA).