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6 protocols using omnimap anti rabbit secondary antibody

1

Immunohistochemical Detection of pAkt in Brain Sections

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The 4-μm brain sections were deparaffinized in an automated system (Discovery XT; Ventana Medical Systems) with EZ Prep solution. A heat-induced antigen retrieval method was used in Cell Conditioning 1 solution. Rabbit primary antibody reacting with pAkt (ab81283; Abcam, Cambridge, MA) was used at a 1:200 dilution in PSS Diluent for antibodies (Ventana Medical Systems) and was incubated for 32 min, followed by OmniMap anti-rabbit secondary antibody (Ventana Medical Systems) for 20 min. For detection, the Discovery ChromoMap DAB Kit (Ventana Medical Systems) was used; slides were then counterstained with hematoxylin, dehydrated, and coverslipped. A BX53 Microscope (Olympus) and cellSens Dimension software were used to obtain pictures with ×10 and ×60 objectives.
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2

Predicting Immune Response Using Radiomic Features

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We selected 25 cases each that were predicted to have high and low immune response by using the value of the radiomic feature in the prognostic modules M2, M9, and M12 that showed the highest absolute correlation to the mean expression of genes in the CTLA4 inhibitory pathway that is supported to be associated with immune activity (Postow et al., 2015 (link); Pardoll, 2012 (link); Wolchok and Saenger, 2008 (link)). In total, 22 cases were available with enough tumor tissue and sufficient staining quality. Tumor cross section slides were stained using a Ventana Discovery XT automated system (Ventana Medical Systems, Tucson, AZ) as per manufacturer's protocol with recommended reagents. Briefly, slides were deparaffinized with EZ Prep solution (Ventana) and a heat-induced antigen retrieval method was used under mild cell conditioning using CC1 antigen retrieval buffer (Ventana). A rabbit primary antibody for CD3, (790–4341, Ventana) was used at supplied concentration and incubated for 16 min. Next a Ventana OmniMap Anti-Rabbit Secondary Antibody was applied to the samples for 16 min and the Ventana ChromoMap kit was used as the detection system. Slides were then counterstained with Hematoxylin and dehydrated. Finally, the slides were cover slipped as per normal laboratory protocol.
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3

Quantifying Tumor-Infiltrating Lymphocytes in Pancreatic Tissue

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Formalin-fixed (10%, 24 h) OPC and OPC-API pancreatic tissue slices, including tumors, were used and sectioned to detect TILs via immunohistochemistry using rabbit anti-mouse-CD3 (Spring Biosciences, Pleasanton, CA, USA), at a dilution of 1:100 for 32 min, and OmniMap anti-rabbit secondary antibody (Ventana, Tuscon, AZ, USA) for 8 min. CD3+ TILs were detected using a ChromoMap Kit used on a Discovery XT automated system (Ventana), following manufacturer’s instructions. Staining was performed at Moffitt Cancer Center (Tampa, FL, USA). Moffitt Cancer Center Pathologist took high magnification (600×) and high-resolution microphotographs of OPC and OPC-API tumor slides (blinded) using an Olympus Model BX43 microscope. Individual CD3+ TILs (denoted by cells enveloped in the brown detection color) were counted as the pathologist instructed. Non-specific binding was not detected using appropriate controls.
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4

CD3 and CD11b Immunohistochemistry in Lung Tissue

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Slides from the lung sections were deparaffinized with EZ Prep solution (Ventana). The heat-induced antigen retrieval method was used in Cell Conditioning 1 Mild (Ventana). The primary rabbit antibody that reacts to CD3 (ab16669, Abcam, Cambridge, MA) was used at a 1:200 dilution in Dako antibody diluent (Carpenteria, CA) and incubated for 32 minutes. The primary rabbit antibody that reacts to CD11b (#LS-C141892, Lifespan Bioscience, Seattle, WA) was used at a 1:700 dilution in Dako antibody diluent (Carpenteria, CA) and incubated for 28 minutes. For both antibodies, the tissue section was exposed to Ventana OmniMap Anti-Rabbit Secondary Antibody for 16 minutes. The detection system used was the Ventana ChromoMap kit, and slides were then counterstained with Hematoxylin. Slides were dehydrated and placed under cover slips as per standard laboratory protocol.
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5

Osteosarcoma Tumor Angiogenesis Quantification

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Paraffin-embedded tumors from the IgG1 control-treated (n = 6) and hSFRP2 mAb-treated (n = 6) metastatic osteosarcoma mice were sectioned at 6 µm, and immunohistochemistry was performed as described previously (34). Briefly, slides were deparaffinized and rehydrated using Discovery wash (950-510, Roche Tissue diagnostics, Indianapolis, IN, USA). Antigen retrieval was performed using EDTA buffer solution for 32 min on the Discovery Ultra staining platform. Endogenous peroxidase was blocked with Discovery Inhibitor solution (760-4840, Roche Tissue Diagnostics), and the tumors were then incubated with CD31 antibody (1:200, #ab28364, Abcam) for 1 h RT. A negative control with no primary antibody added was generated to ensure the specificity of the staining. Slides were then incubated with an HRP-conjugated OmniMap anti-rabbit secondary antibody (1:200, #760-4311, Ventana Medical System, Tucson, AZ, USA) for 20 min at 37 °C, and then precipitated with a DAB substrate following chromomap DAB kit protocol instructions (#760-159, Ventana Medical Systems). Five fields per tissue slice were analyzed from pictures taken at 40× using the EVOS FLc Digital Imaging System (Thermo Fisher Scientific), and hot spots of positively stained cells were counted within each field as previously published [16 (link)]. The numbers obtained for all 5 fields were then averaged.
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6

Immunohistochemical Analysis of Colon Cancer

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A colon cancer TMA block was constructed in the Tissue Core Facility at the Moffitt Cancer Center using a TMA Tissue Arrayer (Beecher Instruments, Estigen, Tartu, Estonia). The diagnosis of each sample was confirmed and the area of interest outlined by a pathologist with interest in GI Pathology before being included in the TMA. TMA sections (3 micron thickness) were immunostained using a Ventana Discovery XT automated system (Tucson, AZ, USA). Briefly, slides were deparaffinized on the automated system with EZ Prep solution (Ventana). The same BAG4 and IL6ST antibodies listed above and CD44 (#HPA005785, Sigma) were incubated at 1:200, 1:800 and 1:1000 dilution, respectively, in Dako antibody diluent (Carpenteria, CA, USA) and for 60, 60 and 32 min, respectively. We used heat-induced antigen retrieval in Ribo CC (Ventana) for BAG4 and Cell Conditioning 1 (Ventana) for IL6ST and CD44. Next, Ventana OmniMap Anti-Rabbit Secondary Antibody was used for 16 min (BAG4), 20 min (CD44), and 8 min (IL6ST). Detection utilized the Ventana ChromoMap kit, and the slides were then counterstained with Hematoxylin.
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