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39 protocols using alexa fluor 594 goat anti rat igg

1

Temporal Neuroimmune Dynamics Post-Induction

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Brain samples were collected 2, 4, and 8 weeks after induction. After being anesthetized with isoflurane inhalation, mice in the 8-week group were perfused through the left cardiac ventricle with heparinized PBS to remove the intravascular blood before brain sample collection. Mice in the 2- and 4-week groups were not perfused. Brain samples were frozen in dry ice, and cut into 20-μm-thick coronal sections, which were then co-stained with antibodies against CD31 (an EC marker, 1:50, Abcam, Burlingame, CA) and CD68 (a macrophage marker, 1:500; AbD Serotec, Raleigh, NC). Positive stains were visualized by incubating the sections with fluorescent-labeled secondary antibodies: Alexa Fluor 488 goat anti-rabbit IgG (1:500, Invitrogen, South San Francisco, CA) for CD 31, and Alexa Fluor 594 goat anti-rat IgG (1:500, Invitrogen) for CD68.
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2

Immunofluorescent Detection of CD19+ Cells

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The lung sections were incubated with anti-CD19, 1D3 (BD), overnight at 4°C and Alexa Fluor 594 goat anti–rat IgG (Invitrogen), followed by anti–IgM-FITC, II/41 (BD). The slides were coverslipped using a mounting medium with DAPI (Vector Laboratories) to identify the nuclei. Images were captured and processed using an epifluorescence microscope (Eclipse 80i; Nikon Instruments Inc.).
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3

Immunofluorescent Staining of Tumor Xenografts

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Frozen sections of tumor xenografts were treated with the purified rat anti-mouse CD31 antibody (BD Pharmingen Cat# 550274, × 100 dilution) and Alexa Fluor 594 goat anti-rat IgG (Invitrogen, x 2,000 dilution) as described previously [43 (link)].
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4

Immunohistochemical Analysis of Muscle Regeneration

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Mice were euthanized on POD 21 for harvesting of the left and right adductor and gastrocnemius muscles. Tissue samples were fixed in 10% formalin, embedded in paraffin, and sectioned. Slides were deparaffinized per standard protocol, and antigen retrieval was performed in EDTA buffer (pH 9.0) at 120°C for 10 minutes. Slides were washed in distilled water and permeabilized with 0.25% Triton-X100 TBS for 15 minutes. Tissue was incubated with Protein Block (ab64226, Abcam, Cambridge, United Kingdom) for 1 hour. Slides were then incubated overnight at 4°C with primary antibodies (5 μg/mL) for E-selectin (148802, BioLegend, San Diego, CA), MyoD (NBP1-54153, Novus Biologicals, Littleton, CO), Ki-67 (SC-7846, Santa Cruz Biotechnology, Dallas, TX), laminin (NBP2-44751, Novus), and Myh7 (NBP2-94079, Novus) followed by Alexa Fluor 488 donkey anti-rabbit IgG (A21206, Invitrogen, Waltham, MA), Alexa Fluor 488 goat anti-mouse (A11029), Alexa Fluor 594 chicken anti-goat IgG (A21468, Invitrogen), or Alexa Fluor 594 goat anti-rat IgG (A11007, Invitrogen) as appropriate (2 μg/mL). Slides were imaged at 20x magnification with a Zeiss Axio Observer inverted microscope (ZEISS, Oberkochen, Germany). For each stain, a blinded observer acquired at least 4 images from 4 sections per mouse (N = 5 per group) and performed cell counting in Fiji.
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5

Comprehensive Immunohistochemical Characterization of Corneal Tissue

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For IDUA staining, Rabbit Polyclonal IDUA antibody (Biorbyt, catalog number: orb157615, dilution 1/50); for GFP staining, Chicken anti GFP antibody (Aves, catalog number: GFP-1020, dilution 1/100); for CD34 staining, mouse monoclonal antibody (clone: B-6) (Santa Cruz, sc-74499, dilution 1/100)), for α-Smooth Muscle Actin staining, mouse monoclonal antibody (R&D, clone #1A4, catalog number MAB1420, dilution 1/100), and for F4/80 marker staining, rat monoclonal antibody, (clone: BM8) (Santa Cruz, sc-52664, dilution 1/100). Secondary antibodies were the following: Alexa Fluor® 594 goat anti-rabbit IgG (A-11012) (Gibco – Invitrogen, Carlsbad, CA), Alexa Fluor® 594 goat anti-chicken IgG (A-11039) (Gibco – Invitrogen, Carlsbad, CA), Alexa Fluor® 594 goat anti-rat IgG (A-11006) (Gibco – Invitrogen, Carlsbad, CA) and Alexa Fluor® 488 goat anti-mouse IgG (A-11001) (Gibco – Invitrogen, Carlsbad, CA). Images from each slide were taken using a Zeiss LSM 780 Confocal Microscope with a 40× objective (Olympus, Tokyo, Japan). Images that comprised the complete human cornea were taken with 10× objective, the title function and then stitched. Images were then processed using Adobe Photoshop. Sections from each tissue were stained with secondary antibody alone as negative control staining in all experiments.
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6

Immune Response to ECM Implantation

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Animal experiments were conducted in accordance with guidelines set by the Johns Hopkins University Animal Care and Use Committee. Bone and collagen tissue ECM particulate was hydrated with saline (100 mg dry wt/0.2 ml) and injected subcutaneously on the dorsum of 6–8 week old female C57BL/6 mice. Animals were sacrificed after 1 week, implants explanted, fixed in formalin, and embedded in paraffin for sectioning. Sections were then deparaffinized, rehydrated, and immunolabeled for the pan-macrophage marker F4/80 and the M1 marker iNOS. Antigen retrieval was conducted in citrate (10 mM, pH 6) for 30 min in a vegetable steamer, and rinsed with TBS in 0.05% Tween-20. Sections were blocked with 1% bovine serum albumin, 2% goat serum, and 0.05% Tween-20 for 1 hour. Sections were then incubated with primary antibodies against F4/80 (rat monoclonal [BM8] diluted 1:100, ab16911, abcam) and iNOS (mouse monoclonal [4E5] diluted 1:200, ab129372, abcam) overnight at 4°C in blocking solution. Sections were washed and probed with FITC goat anti-rabbit IgG (1:250, Jackson Immuno) and Alexa Fluor-594 goat anti-rat IgG (1:250, Invitrogen) secondary antibodies diluted in blocking solution for 1.5 hours. ECM autofluorescence was then blocked by treatment with 0.1% Sudan Black B in 70% ethanol for 20 min. Sections were counterstained with DAPI for 5 min, washed, coverslipped, and imaged.
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7

In Vitro and In Vivo Analyses of RBC Binding with FITC-Labeled TER119-Coated Liposomes

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For in vitro analysis of RBC binding with FITC-labeled TER119-coated liposomes RBC were incubated with the liposomes, washed by centrifugation, adsorbed on glass slides, washed and mounted. In in vivo studies animals were sacrificed; lungs were harvested, immersed in OCT, and frozen by liquid N2. Frozen tissues were cut using Cryostat with 10-20 μm/slice. Samples were fixed with 4% paraformaldehyde for 10 min and permeabilized with 0.3% Triton X-100 for 15 min prior staining with antibodies. Leukocytes were stained with rabbit anti-mouse CD45 antibody (Abcam, #ab10558) followed by Alexa Fluor 647 labeled anti-rabbit IgG. Liposomes were stained with Alexa Fluor 594 goat anti-rat IgG (Invitrogen). Microscopy studies were performed on a confocal laser scanning microscope Leica TCS-SP8 (Leica, Germany) using HC PL APO CS2 63x/1.40 Oil objective and 488/552/638 lasers. Image analysis was performed using Volocity 6.3 Cellular Imaging & Analysis.
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8

Histological Analysis of AVM Lesions

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Mice were anesthetized with isoflurane inhalation and perfused with heparin/PBS to remove blood. Brain samples were harvested and frozen in dry ice, then sectioned into 20 µm sections. The location of AVM lesions was first identified through staining 1 of every 10 sections with lectin (1∶200; Vector Laboratories). Sections containing dysplastic vessels were then co-stained with primary antibodies against CD31 (1∶50; Abcam) and CD68 (1∶50; AbD Serotec). Each protein was subsequently visualized using fluorescently labeled secondary antibodies: Alexa Fluor 488 goat anti-rabbit IgG (1∶500; Invitrogen) for CD31, and Alexa Fluor 594 goat anti-rat IgG (1∶500; Invitrogen) for CD68. ENG expression was identified by an antibody against ENG/CD105 (1∶50; BD Pharmingen) and visualized by a biotin-conjugated secondary antibody (anti-rat IgG, 1∶500; Vector Laboratories), using the standard ABC method (Vector immunodetection kit; Vector Laboratories). Prussian blue staining was performed according to the protocol provided by the company (Iron Stain Kit; Sigma-Aldrich).
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9

Immunofluorescence Analysis of Organoid Samples

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Organoid immunofluorescence was performed in accordance with previously published methods80 (link). Briefly, whole organoids were dissociated from matrigel, washed in PBS and fixed with 4% PFA on ice. Organoids were blocked for 1 hr at room temperature (1% BSA/PBS) and stained overnight at 4 °C with the following primary antibodies: rat anti-SCA1/LY6A (1:100; R&D Biosystems, 177228) and rabbit anti-YAP (1:100; Cell Signaling Technology, 4912). Organoids were exposed to Alexa Fluor 488 Goat anti-rabbit IgG or Alexa Fluor 594 goat anti-rat IgG (Invitrogen, 1/500) 2 hours at room temperature and counterstained with DAPI. Z-stack fluorescent and brightfield images were taken on a Zeiss 710 confocal microscope. Image analysis and Z-projection were performed using FIJI software and brightness and contrast settings were maintained between control and test images.
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10

Immunofluorescent Quantification of F4/80+ Cells

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Tissue sections (4 µM thick) were dewaxed, and then heat-induced epitope
retrieval performed. Sections were blocked with the Dako Serum-free protein
block (Agilent) for 30 min. Next, F4/80 primary antibody diluted in Dako
Antibody Diluent (Agilent) was applied overnight at 4°C. The following day,
sections were incubated in Alexa-Fluor-594 goat-antirat IgG (Invitrogen, A11007)
diluted 1:400 in Tris-buffered saline for 1 h at room temperature. Sections were
stained with Hoechst (Sigma, Cat 14533) for 10 min at room temperature and
mounted with Gelvatol medium. Fluorescence was imaged, and the number of
positive cells quantified using the Cellinsight CX 7 High-Content Screening
Platform (Thermo Fisher Scientific).
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