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8 protocols using af594

1

Immunohistochemical Analysis of GC Tissues

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The M-HFn nanoparticle-based IHC assay for GC tissues was performed as previously reported12 (link). As negative controls, the sections were processed using the same protocol, except that they were not incubated with the M-HFn nanoparticles. The staining of TfR1 was examined and scored by two independent pathologists under microscopy, who were blind to the patient clinical data. Immunoreactivity score together with the staining intensity were used to assess the staining of TfR1. Finally, the staining levels of TfR1 expression were ascribed to − and +, low expression; ++ and +++, high expression.
For IHC, primary antibodies were used to detect anti-transferrin receptor antibody (anti-TfR1, Abcam, Cambridge, UK), PCNA (Dako, Carpinteria, CA, USA), and Ki67 antibody (Abcam, Cambridge, UK). For IF, primary antibodies were used to detect CD44 (Dako, Carpinteria, CA, USA) and 1B50-1 (anti-CACNA2D1), gifted by Prof. Zhang, Peking University, with visualization using fluorescein AF488 and AF594 (Jackson Alexa Fluor). DAPI was used to detect nuclei.
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2

Quantifying CD39-Expressing Cell Interactions

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CD39-expressing CHO cells were mixed 1:1 with CFSE-labeled wild type CHO cells and seeded in 96-well microplates (Greiner) at 8000 cells/well in 100 μL of medium and cultured overnight. After incubation, 50 μL of medium was replaced with 50 μL of original (six 96-well plates, 576 samples) or serially diluted (×2, 12 times, 12 positive samples) hybridoma supernatant samples in each well. After incubation for 60 min at 37°C and two washes with PBS, cells were fixed with 4% PFA for 20 min and washed twice. Subsequently, 100 μL of secondary Donkey anti-mouse IgG (H+L) antibodies (2.5 μg/mL) labeled with AF594 (Jackson ImmunoResearch) were pipetted into each well, incubated for 60 min at room temperature, and washed twice. Finally, cells were stained with 100 μL of 2 μg/mL of Hoechst for 30 min, and then washed once prior to Celigo image cytometric analysis.
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3

Immunostaining Protocol for Mesenteric Vascular Structures

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Mesenteries were fixed in 4% paraformaldehyde at room temperature for 2 h and stained as previously described (Stanczuk et al., 2015 (link)). The following primary antibodies were used: mouse anti-α-smooth muscle actin-Cy3 (Sigma-Aldrich, C6198, 1:250), rat anti-endomucin (V.7C7) (Santa Cruz, SC-65495, 1:200), rat anti-CD41-FITC (eBioscience, 11-0411-81, 1:50), rabbit anti-collagen IV (Bio-Rad, 2150-1470, 1:500), chicken anti-GFP (Abcam, ab13970, 1:200), goat anti-neuropilin 2 (R&D Systems, AF567, 1:200), hamster anti-PECAM1 (Millipore, MAB1398Z, 1:1000), rat anti-PECAM1 (BD Pharmingen, 553370, 1:1000), rat anti-PECAM1-AF594 (BioLegend, 102520, 1:100), rabbit anti-human PROX1 (Stanczuk et al., 2015 (link); 1:200), rat anti-TER-119 (eBioscience, 145921, 1:200), rat anti-TER-119-AF647 (BioLegend, 116218, 1:50), goat anti-VE-cadherin (Santa Cruz, SC-6458, 1:200) and anti-podoplanin (Developmental Studies Hybridoma Bank at the University of Iowa, clone 8.1.1, 1:800). Autofluorescence signal at 550-600 nm wavelength was used for visualization of RBCs. Secondary antibodies conjugated to AF488, AF594, AF647 or Cy3 were from Jackson ImmunoResearch, and all were used at 1:300.
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Immunofluorescence and Flow Cytometry Protocols

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The details of primary antibodies used for immunofluorescence of whole mount tissues and flow cytometry are provided in Table S2. Secondary antibodies conjugated to AF488, AF594, AF647 or Cy3 were obtained from Jackson ImmunoResearch and used in 1:300 dilution (Table S2).
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5

Visualizing Inflammasome Proteins in Tissues and Cells

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Indirect (two step) immunofluorescence of inflammasome proteins in tissue [17 (link), 27 (link)] and cells [16 ] was performed according to previously published protocols. Five commercial antibodies (Ab1–5) raised in different species against different immunogenic peptides derived from human AIM2 were used in the study and listed in Table S1. Other primary antibodies, directed against human cleaved IL-1β (goat polyclonal), mouse cleaved IL-1β (goat polyclonal), and anti-ASC (mouse monoclonal) were from Santa Cruz. The specificity of the antibodies to cleaved human and cleaved mouse IL-1β was confirmed by pre-incubation and blocking specific labelling with the immunogen peptides. The secondary antibodies were AF488, AF594 and AF647-conjugated donkey serum IgG F (ab’)2 fragments, obtained from Jackson ImmunoResearch (West Grove, PA, USA).
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6

Characterization of Tumor-Infiltrating Lymphocytes

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Tumoral tissue was embedded in Tissue-Tek (Sakura) and sections (5 μm) were cut onto charged glass slides (Superfrost Plus Yellow) and rehydrated. Antigen retrieval was performed in citrate buffer pH 6.0 (sodium citrate 10 μM) at 90°C for 20 min. The sections were permeabilized (bovine serum albumin 10 mg/ml, horse serum 5%, Triton 0.5%, and sodium azide 0.02%) for 2 h and incubated with anti-CD8-FITC (BioLegend Cat# 100705, RRID:AB_312744), anti-CD103 (BioLegend Cat# 121426, RRID:AB_2563691), anti-PD-1-APC (BioLegend Cat# 135209, RRID:AB_2251944), anti-TIM-3-PE/Dazzle (BioLegend Cat# 134014, RRID:AB_2632738), anti-GZMB (BioLegend Cat# 372222, RRID:AB_2728389), anti-IFNγ-PE and anti-TCF-1 primary antibodies at room temperature (RT) for 18 h. The anti-CD103, anti-GZMB and anti-TCF-1/7 mAbs were revealed with a secondary antibody, either AF-647 (Jackson ImmunoResearch Labs Cat# 711-585-152, RRID:AB_2340621) or AF-594 (Jackson ImmunoResearch Labs Cat# 711-605-152, RRID:AB_2492288). The nuclei were counterstained with Hoechst (Invitrogen) for 10 min. The sections were mounted with Vectashield (Vector Laboratories).
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7

Flow Cytometry Analysis of CHO Cells

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CHO cells were collected by EDTA-trypsin digestion, washed with PBS, incubated with hybridoma culture supernatants at 4°C for 30 min. Cells were then washed with sorting buffer (PBS supplemented with 1% FBS) and stained with the secondary goat anti-mouse IgG (H+L) antibodies labeled with AF594 (Jackson ImmunoResearch) for 30 min at 4°C. Fluorescently labeled cells were washed and analyzed using the FACSCalibur for flow cytometry-based analysis.
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8

Immunofluorescence Staining for GFP, CD44, and Macrophages

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For 1-mm sections, a standard immunofluorescence protocol was performed. 14, 46 For 1000-1500-mm-thick slices, we used a recently published protocol. 13 The following antibodies were used: polyclonal guinea pig anti-mouse GFP (1:500; Synaptic Systems, 132004, Goettingen, Germany), AlexaFluor (AF)647-conjugated polyclonal rat anti-mouse/human CD44 (1:200; BioLegend, 103018, San Diego, CA), polyclonal goat anti-guinea pig AF594 (1:200; Jackson Immuno Research Laboratories, Cambridge, UK, 106-585-003), polyclonal rabbit anti-mouse p57 (1:200; SC8298; Santa Cruz Biotechnology, Dallas, TX), polyclonal goat anti-mouse Synaptopodin or SNP (1:400; SC21537; Santa Cruz Biotechnology), polyclonal donkey anti-rabbit AF555 (1:200; Life Technologies, A31572, Carlsbad, CA), t e c h n i c a l n o t e s polyclonal chicken anti-goat AF488 (1:200; A2467; Life Technologies), and AF594-conjugated polyclonal rat anti-mouse F4/80 (1:50; BioLegend, 123140).
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