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13 protocols using goat anti rat igg

1

In situ Proximity Ligation Assay

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PLA was performed using the Duolink in situ kit (Olink Bioscience) according to the manufacturer’s instructions with the following modifications: Incubation with PLA probes was for 2 hours at 37°C; ligation step was performed for 45 min at 37°C; amplification step was extended to 2 hours at 37°C with a concentration of polymerase of 1/60. Anti-rat PLA probes were generated according to the manufacturer’s instructions using the Duolink Probemaker (Olink Bioscience) and goat-anti rat IgGs (Santa Cruz).
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2

Proximity Ligation Assay of GluN1 and D1R

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Brain slices were prepared as previously described21 (link) and proximity ligation assay (PLA) was performed using the Duolink in situ kit (Olink Bioscience, Uppsala, Sweden) according to the manufacturer's instructions with the following modifications: PLA probes incubation was for 2 h; ligation was performed for 45 min; amplification step was extended for 2 h with a concentration of polymerase of 1/60 all at 37°C. Striatal primary cultured cells were plated into 8-μ well plates (LabTek, Dutscher, Brumath, France). Blocking (1 h at room temperature) and primary antibody (overnight at 4 °C) incubations were performed in a 3% bovine serum albumin (Sigma Aldrich) and 0.2% Triton X-100 solution. Rabbit anti-GluN1 (ab17345, Abcam, Cambridge, MA, USA) and rat anti-D1R (D2944, Sigma Aldrich) were diluted (1:500) in the blocking solution. The anti-rabbit (+) PLA probe (1:5) along with an anti-rat (−) probe (1:100) were diluted in the blocking solution. Anti-rat PLA probes were generated according to the manufacturer's instructions using the Duolink Probemaker (Olink Bioscience). Goat-anti-rat IgGs (Santa Cruz, Heidelberg, Germany) were used. Cells were mounted in FluorSave (Calbiochem). Image acquisition and quantification are detailed in the Supplementary Information section.
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3

In situ Proximity Ligation Assay

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PLA was performed using the Duolink in situ kit (Olink Bioscience) according to the manufacturer’s instructions with the following modifications: Incubation with PLA probes was for 2 hours at 37°C; ligation step was performed for 45 min at 37°C; amplification step was extended to 2 hours at 37°C with a concentration of polymerase of 1/60. Anti-rat PLA probes were generated according to the manufacturer’s instructions using the Duolink Probemaker (Olink Bioscience) and goat-anti rat IgGs (Santa Cruz).
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4

Dual-Antigen Proximity Ligation Assay

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Dual-antigen recognition PLA experiments were conducted as described in Trifilieff et al. (2011) (link). Briefly, PLA was performed using the DuoLink in situ kit (Olink Bioscience, Uppsala, Sweden) according to the manufacturer’s instructions with the following modifications: incubation with PLA probes and the ligation step were extended to 2h and to 45 min, respectively; the amplification step consisted of a 2h incubation at 37°C with a 1/60 concentration of polymerase. Anti-D1R (rat) and anti-D2R (rabbit) primary antibodies were used at a concentration of 1:200. The anti-A2AR primary antibody (mouse) was used at a dilution of 1:1000. Subsequent secondary labeling of the D2R and A2AR for this assay was accomplished with the use of kit-provided anti-rabbit and anti-mouse PLA probes, respectively, while the D1R was detected using an anti-rat PLA probe generated according to the manufacturer’s instructions using the DuoLink Probemaker kit (Olink Bioscience) and goat anti-rat IgGs (Santa Cruz Biotechnology, Dallas, TX). For this assay, slices were coverslipped with Fluorsave (Millipore, Billerica, MA).
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5

Tumor-Penetrating Ability of Nanoparticles

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Immunofluorescence method was used to investigate the tumor-penetrating ability of Fe3O4@SiO2@mSiO2/DiO-(Gd-DTPA)-PEG-RGE NPs. The Fe3O4@SiO2@mSiO2/DiO-(Gd-DTPA)-PEG-RGE NPs were i.v. injected to U87MG tumor-bearing mice (n = 3). The mice were sacrificed 8 h post-injection, and the tumor tissues and main organs (including heart, liver, spleen, lung, and kidney) were collected, fixed, dehydrated, and frozen in acetone/dry ice mixture. The frozen samples were further cut to sections (10 μm) with a cryostat (CM3050 S, Leica, Germany). The sections were stained with rat anti-mouse CD31 (1:10, R&D Systems), followed by rhodamine labeled goat anti-rat IgG (1:100, Santa Cruz) and Hochest33342, and then observed using a confocal laser scanning microscope (CLSM, TCS SP5, Leica, Germany).
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6

Western Blot Analysis of Vesicular Proteins

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One microgram of vesicular proteins was separated by SDS-PAGE and then transferred to a 0.2 µm polyvinylidene difluoride membrane. The membrane was blocked with 5% non-fat milk or 3% skim milk in Tris-buffered saline with 0.05% Tween-20, incubated with primary antibody followed by secondary antibody conjugated with horseradish peroxidase, and subjected to the enhanced chemiluminescence. The membrane was washed three times by Tris-buffered saline with 0.05% Tween-20 after each incubation. Goat anti-actin (1:1000 dilution, SC-1616), rabbit anti-GAPDH (1:1000 dilution, SC-257,780), goat anti-mouse IgG (1:5000 dilution, SC-516,102), goat anti-rabbit IgG (1:5000 dilution, SC-2004), donkey anti-goat IgG (1:5000 dilution, SC-2020) and goat anti-rat IgG (1:5000 dilution, SC-2006) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Mouse anti-CD81 (1:1000 dilution, 555,675) and mouse anti-calnexin (1:1000 dilution, 610,523) antibodies were from BD Biosciences (San Diego, CA). Goat anti-ICAM1 (1:1000 dilution, BBA17) antibody was obtained from R&D Systems (Abingdon, UK). Mouse anti-60 S ribosomal protein L14 (RPL14) (1:1000 dilution, ab89095) antibody was from Abcam (Cambridge, MA). Mouse anti-tubulin (1:1000 dilution, T6074) antibody was from Sigma (St. Louis, MO). Rabbit anti-H2B (1:1000 dilution, 07–371) antibody was obtained from Millipore (Darmstadt, Germany).
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7

Immunofluorescence Detection of EV71 Infection

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Vero cells infected with EV71 H3-TY were incubated in a 96-well plate at 35°C in 5% CO2. When CPEs were observed (at least 25%), cells were fixed with precooled acetone. Antibodies diluted to 1:100 in PBS were added to the plates blocked with 1% BSA in PBS, and incubated overnight at 4°C. After washing five times with PBS containing 0.01% Tween-20 (PBS-T), FITC-conjugated goat anti-mouse IgG, goat anti-rat IgG, or goat anti-rabbit IgG (diluted 1:50 in PBS-T; Santa Cruz Biotechnology, Santa Cruz, CA, USA) were added and the plates were incubated for 1 h at 37°C. After washing five times with PBS-T, fluorescent images were visualized and captured using a DM BL2 fluorescence microscope (Leica Microsystems GmbH, Wetzlar, Germany).
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8

Quantitative Analysis of CCP6 Protein

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Approximately 1 mm3 of each tissue samples were retrieved from liquid nitrogen and grinded and homogenized in a cell lysis buffer (Beyotime, Beijing, China) and then centrifuged at 10000 rpm for 30 min 4°C to remove cell debris. A Bradford protein assay kit (Bio-Rad, Hercules, CA, US) was used to quantify the protein concentration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was to separated proteins in 12% SDS-PAGE gel and transferred onto PVDF membranes (Beyotime, Beijing, China). After 2 h 5% milk blocking, the PVDF membranes were incubated with an anti-CCP6 (Santa Cruz Biotechnology, Santa Cruz, CA, US) or anti-β-actin antibody (Sigma-Aldrich, St Louis, MO, USA) at 4°C overnight. On the next day, the membranes were further incubated with a goat anti-Rat IgG (Santa Cruz Biotechnology) for 2 h at the room temperature and then incubated with a chemiluminescence (ECL; Beyotime) kit to detect protein signals. The CCP6 protein density in each sample was normalized to the level of β-actin. Data and figures were analyzed with SPSS 18.0 software and GraphPad Prism Version 5.0, differences between groups were statistically evaluated by sample one-tailed Student's t-test, p value < 0.05.
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9

Monoclonal Antibody Purification and Characterization

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Monoclonal antibodies (mAbs) 1E3 (anti-Tn; Clausen and Hakomori, Unpublished Data), B72.3 (anti-STn) [22 (link)] and 3C9 (anti-T) [23 (link)] were purified from hybridoma culture media. CD44 (156-3C11) mAb was obtained from Cell Signalling Technology (Leiden, The Netherlands), CD44v9 (RV3) mAb from Abnova (Taiwan, China), CD44v (CD44v6 – MA54) from Invitrogen (Waltham, MA, USA) and tubulin (DMA1A-9) mAb from Merck (Darmstadt, Germany).
Secondary antibodies goat anti-mouse and donkey anti-rat Alexa Fluor® 488 and goat anti-mouse Alexa Fluor® 594 were purchased from Invitrogen; horseradish peroxidase-conjugated goat anti-mouse IgG from Jackson ImmunoResearch (Cambridge, UK) and goat anti-rat IgG from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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10

Preparation and Validation of PIV3 Antibody

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Custom rat antibody was made commercially (Biosynthesis, Inc., Lewisville, TX) against the synthetic peptide KRNQEINQLISPRPSTSLNS of PIV3 nonstructural protein C as described previously (Rabbani et al., 2016 (link)). Commercial primary antibodies used in immunoblotting included PIV3 HN antibody (Abcam; cat# ab49756), IDO antibody (Santa Cruz; cat# sc-25809), mouse glyceraldehyde-3-phosphate dehydrogenase (GAPDH) antibody (G-9; Santa Cruz; cat# sc-365062). The corresponding horseradish peroxidase-conjugated secondary antibodies were purchased from Santa Cruz Biotechnology: goat anti-mouse IgG (cat# sc-2031), goat anti-rabbit IgG (cat# sc-2030), and goat anti-rat IgG (cat# sc-2032). Lysis of cells, SDS-PAGE and immunoblotting were also performed as described (Rabbani et al., 2016 (link)).
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