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3 protocols using cytokeratin mnf 116

1

Comprehensive Histological Evaluation of Tissues

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Trichrome and periodic acid Schiff (PAS) using standard histologic techniques. Tissue was also stained with antibodies to collagen III (BioGenex, San Ramon, CA; Monoclonal clone HWD1.1; at 1:80 titration), cytokeratin AE1/AE3 (Dako, Carpinteria, CA; prediluted), Cytokeratin CAM 5.2 (BD Biosciences, San Jose, CA; prediluted) cytokeratin cocktail (AE1/AE3;CAM5.2), cytokeratin MNF-116 (Dako; at 1/100), and CD34 (Dako; Monoclonal clone QBEND; at 1:320 titration). IHC was performed with automated stainers similar to methods previously published [1 (link), 26 ].
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2

Immunohistochemical Profiling of FFPE Tumor Tissue

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Tumour tissue and the agarose-embedded close-to-patient cancer cells were formalin fixed and paraffin embedded (FFPE) before 4 μm sections were cut for both H&E and immunohistochemistry (IHC) analysis. IHC was performed using standard techniques and in line with the manufacturer's instructions for the following primary antibodies: Cytokeratin (MNF116, DAKO), EpCam (Ber-EP4, DAKO), CD44 (DF1485, DAKO), p53 (DO-7, DAKO), Vimentin (V9, DAKO), TFF3 (Abcam), and ALDH1A1 (EP1933Y, Abcam) (see online supplementary method S6). Sections were viewed with a Leica DMLB Bright-field Microscope (Leica-microsystems, Milton Keynes, UK) and images acquired with Leica QWin Standard v3 software. The presence of any characteristically stained cells was considered positive with respect to negative controls, and confirmed by a second blinded individual.
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3

Comprehensive Immunohistochemistry Protocol

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For immunohistochemistry, 2 μm thick sections were cut and antigens retrieved in an epitope retrieval solution of pH 8 (RE7116; Novocastra, Newcastle, UK) at 68 °C for 17 h in a stirred water bath. The antibody clones, dilutions and sources are as follows: CD99 (12E7, 1:25; Dako, Ely, UK), vimentin (V9, 1:100, Novocastra), CD31 (JC70, 1:100, Dako), CD34 (QBend10, 1:50, Dako), cytokeratin AE1/AE3 (1:100, Dako), CD45 (2B11+PD7/26, Dako), cytokeratin MNF116 (1:50, Dako), desmin (D33, 1:100, Dako), α-smooth muscle actin (SMA) (1A4, 1:200, Dako), epithelial membrane antigen (EMA) (E29, 1:100, Dako), HMB-45 (1:200, Dako), S100 (NCL-L-S100p, 1:1000, Novocastra), WT1 (C-19, 1:500, Santa Cruz, Insight Biotechnology Limited, PO Box 520, Wembley, Middlesex,UK), TLE1 (M-101, 1:50, Santa Cruz), ERG (Erg-1/2/3 C-1; 1:50, Santa Cruz), INI1 (1:25, BD Transduction Laboratories (BD Biosciences), Becton Dickinson UK, Oxford, UK), BCOR (C-10, 1:50, Santa Cruz), ETV4 (16, 1:50, Santa Cruz) and Ki-67 (MIB1, 1:200, Dako).
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