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12 protocols using summit version 4

1

Annexin V-FITC/PI Apoptosis Assay

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The PCD of the Raw 264.7 cells and the patient isolated monocytes were monitored by flow cytometry using double staining with Annexin V-fluorescein isothiocyanate and propidium iodide (PI; Apoptosis Detection kit; Immunostep, Salamanca, Spain), according to the manufacturer's instructions. The fluorescence was measured with a Cyan ADP cytometer and Summit version 4.3 software (Beckman Coulter, Fort Collins, CO, USA), and was subsequently analyzed with FlowJo 7.6 software (TreeStar Inc., Ashland, OR, USA). This technique was used to assess the effect of the treatments on cell viability. Debris were excluded from the plot based on the scatter (FSC vs. SSC) and the apoptotic (Annexin V positive, A+; PI negative, PI and positive, PI+) and the necrotic (A and PI+) cells were characterized based on the fluorescence emitted.
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2

Enumeration of Tumor Endothelial Cells

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Tumor specimens were prepared as single cell suspensions as previously described [48 ]. Cells from tumor specimens were immunostained with CD45-APC-Cy7, CD31-APC, and VEGFR2-PE (BioLegend, San Diego, CA). Endothelial cells were defined as CD45–/CD31+/VEGFR2+. At least 100,000 events were collected for each sample. The experiments were performed using Cyan-ADP flow cytometer and analyzed by Summit Version 4.3 software (Beckman Coulter, Switzerland).
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3

Flow Cytometry of Live Parasites

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The flow cytometry experiments were performed on live parasites, using a CyAn flow cytometer (Beckman Coulter, Inc.), and data were collected by using Summit version 4.3 software (Beckman Coulter, Inc.) and analyzed with FlowJo (LLC). A minimum of 10,000 events were collected for parasites with a single fluorescence peak, and a minimum of 20,000 events were collected for fluorescent parasites with two or more fluorescence peaks. An empirical T. cruzi gate was applied to the collected events based on the forward and side scatterplot, and a singlet gate was also applied.
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4

MET Receptor Expression Analysis

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Drug-treated and control vehicle-treated cells were trypsinized and collected by centrifugation. The cells were washed with PBS three times and incubated with an anti-MET antibody (1:50, #5631 Cell Signaling Technology) for 1 hour at room temperature. After 3 washes with PBS, cells were incubated in FITC-conjugated goat anti-mouse IgG (1:500, Millipore) or Alexa Fluor 633-conjugated goat anti-mouse secondary antibodies (1:500, Invitrogen)for 1 hour at room temperature and washed in PBS. The stained cells were measured on a Legacy MOFLOs and analyzed using Summit version 4.3 software (Beckman Coulter).
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5

Annexin V-FITC Apoptosis Assay

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Apoptosis of Jurkat cells was determined using an Annexin V-fluorescein isothiocyanate (FITC) kit (Sigma-Aldrich) according to the manufacturer’s instructions without modifications, followed by flow cytometric analysis in a BD flow cytometer equipped with an argon laser (Cyan ADP; Dako Denmark A/P, Glostrup, Denmark) and with emitting excitation light at 488 nm. The data were analyzed using Summit version 4.3 software (Beckman Coulter, Inc., Brea, CA, USA).
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6

Cell Cycle Analysis of IL-31-Treated Cells

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MC38 or CT-26 cells were cultured with 100 ng/ml rmIL31 or vehicle control for 48 hours. Cells were detached and re-suspended in 100 μl PBS. Cells were fixed by slowly adding the suspension to a tube containing 1 ml 70% ethanol with gentle vortexing. Cells were incubated on ice for 20 min, centrifuged and re-suspended in 1ml of Propidium Iodide (PI) master mix containing 40 μg/ml PI (BioLegend, Inc., USA), 10 μg/ml RNase (Sigma-Aldrich), and 950 μl PBS. After a 30 min incubation at room temperature, samples were analyzed with a Cyan-ADP flow cytometer and Summit Version 4.3 software (Beckman Coulter, Switzerland) using linear scale histogram.
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7

IL-31 Induced Apoptosis Assay

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MC38 or CT-26 cells were cultured with 100 ng/ml rmIL31 or vehicle control for 48 hours. The cells were detached and re-suspended in 60 μl Annexin V Binding Buffer (MBL, Japan). Subsequently, 2.5 μl of Annexin V-FITC antibody (Bio Legend, Inc., USA) and 2.5 μl of 7-Aminoactinomycin D (7-AAD) (Sigma-Aldrich, USA) were added and samples were incubated for 15 min at RT in the dark. Annexin V Binding Buffer (300 μl) was then added to each sample. Samples were analyzed with a Cyan-ADP flow cytometer and Summit Version 4.3 software (Beckman Coulter, Switzerland).
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8

Quantifying HER-2 Expression on Cell Lines

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For HER-2 cell surface staining with trastuzumab antibody (Herceptin; Roche, Basel, Switzerland), titration assays were performed by indirect immunofluorescence using as targets SKBR3, BT474 and MCF-7 cell lines. In particular, 2 × 105 cells/sample were incubated with different concentrations (2, 0.2, 0.02, 2 × 10−3 and 2 × 10−4 µg/ml) of the mAb for 30 min at 4 °C. After washing in FACS buffer, an Alexafluor 647-conjugated goat anti-human IgG secondary antibody (Molecular Probes, Inc. Eugene, OR, USA) was added and incubated for 30 min at 4 °C. After 2 washes, the cells were analyzed by flow cytometry on a CyAn-ADP-Flow-Cytometer (Beckman-Coulter); 5000 cellular events were analyzed per sample. Data were analyzed using Summit version 4.3 Software (Beckman-Coulter).
Results were expressed as mean ratio of relative fluorescence intensity (MRFI), calculated as follows: mean fluorescence intensity (MFI) of HER-2 staining/MFI of secondary antibody staining.
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9

Flow Cytometry Immunophenotyping of Tumor Infiltrating Cells

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Cell suspensions were assessed for T cells, macrophages, neutrophils and their subpopulations thereof using flow cytometry, as described previously [24 (link)]. Briefly, tumors removed from tumor-bearing mice were prepared as single-cell suspensions as previously described [35 (link)], and then immunostained with the following antibody mixture: CD3ε for T cells, F4/80 for macrophages, CD11b, Ly6G and Ly6C for neutrophils. Mature neutrophils were identified as CD11b+Ly6C(high)Ly6G+, and immature neutrophils as CD11b+Ly6C(low)Ly6G+. Flow cytometry experiments were performed using BD LSRFortessa™ (BD Bioscience) flow cytometer and analyzed with Summit version 4.3 (Beckman Coulter).
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10

High-throughput Flow Cytometry Protocol

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A minimum of 250,000 events were collected for each sample on a CyAn ADP using Summit, version 4.3 (Beckman Coulter, Fullerton, CA, USA). Where appropriate, fluorescence minus one controls were used to establish gating measures. FlowJo flow cytometry analysis software, version 9 (Tree Star, Ashland, OR, USA) was used for analyses.
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