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32 protocols using af555

1

Angiogenesis Assay with Modified Immune Cells

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Eight hundred thousand B2m−/−Ciita−/− Cd47 tg miECs, miSMCs or miCMs in 1:1 diluted Matrigel (Corning) were injected into allogeneic BALB/c mice. Matrigel plugs were recovered after 1, 2, 3, 4, 5, 6 and 8 weeks and fixed in 4% paraformaldehyde in PBS with 1% glutaraldehyde for 24 h. Samples were dehydrated, embedded in paraffin and cut into sections of 5 µm thickness. For histopathology, sections were stained with hematoxylin and eosin (Carl Roth) and images taken with an inverted light microscope. Origin of cells was demonstrated with immunofluorescence staining. Sections were rehydrated, and underwent antigen retrieval and blocking. Samples were incubated with antibodies against luciferase (ab21176), SMA (ab21027, Abcam), VE-Cadherin (SC-6458) or α-sarcomeric actinin (EA-53, Abcam) and a corresponding secondary antibody conjugated with AF488 or AF555 (Invitrogen). Cell nuclei were counterstained with DAPI and images taken with a Leica SP5 laser confocal microscope (Leica).
For co-staining experiments of miECs and immune cells, primary antibodies were used against VE-Cadherin (SC-6458, Sigma) and CD3 (ab16669, Abcam), followed by the corresponding secondary antibody conjugated with AF488 or AF555 (Invitrogen).
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2

Multi-color Flow Cytometry of Immune Cells

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Antibodies against CD19 (clone HIB19, AF647, #302220), CD20 (clone 2H7, AF647, #302318), CD38 (clone HIT2, AF488, # 303512), CD138 (clone MI15, PE, #356504 and unconjugated, #356502) from BioLegend (London, United Kingdom); IFN-γ (clone B27, FITC, # 554700) from BD Biosciences (Heidelberg, Germany), and CD8 (clone BW135/80, VioBlue, # 130–094–152) from Miltenyi as well as 7-AAD to exclude dead cells from analysis were used. For dSTORM-microscopy, an anti-CD138 antibody was conjugated to AF555 (ThermoFisher Scientific). Flow analyses were performed with a FACS Canto II (BD) machine and analyzed using FlowJo software (TreeStar, Ashland, OR).
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3

Optogenetic Interrogation of Insular Circuitry

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To measure the dynamic properties of the IC-BLA or IC-CeM synapses, AAV9/2-CaMKIIɑ-hChR2(E123A)-eYFP-WPRE was injected in the IC (Fig. 4a). hChR2(E123A) is the hChR2 variant CheTA 2.0 for ultrafast optogenetic control52 (link),53 (link). To analyze the intrinsic property of the insular neurons projecting to the BLA and CeM, CTB coupled to AF555 or AF647 (Fischer Scientific) were injected in the BLA or CeM, respectively, to label the insular neurons projecting to the BLA or CeM (Fig. 4h–j).
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4

Comprehensive Immunostaining Protocol

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The antibodies used were anti-α-tubulin (YL1/2; rat; ab6160; Abcam), anti–β-catenin (mouse; #610154; BD Transduction), anti-LRP6 (EPR2423(2); rabbit; ab134146; Abcam), anti-NANOG (rabbit; RCAB002P-F; Reprocell), anti-OCT3/4 (mouse; #611202; BD Transduction), anti-EOMES (rabbit; ab183991; Abcam), anti-GriA3 (mouse; MAB5416; Sigma-Aldrich), anti-GriA4 (rabbit; AB1508; Sigma-Aldrich), anti-GriK1 (rabbit; AGC-008; Alomone Laboratories), anti-GriK3 (rabbit; AGC-040; Alomone Laboratories), anti–N-cadherin (mouse; #33-3900; Thermo Fisher Scientific), anti–E-cadherin (DECMA-1; rat; ab11512; Abcam), anti-GFP (chicken; GFP-1020; Aves), anti-mCherry (goat; #200-101-379; Rockland), and AF488, AF555, or AF647-conjugated secondary antibodies (Thermo Fisher Scientific).
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5

Fluorescent Labeling of Immune Markers

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LysoTracker Red DND-99, cholera toxin subunit B (CTB)-Alexa Fluor (AF)555 or AF647 conjugates (Cat. No A20187, A10470, and A20186), and anti-rabbit IgG-AF647 antibody were from ThermoFisher Scientific. Unlabeled anti-TCR Vγ3 (Vγ5 according to Tonegawa’s nomenclature) antibody (clone 536) was from Santa Cruz Biotechnology and its isotype control (Syrian hamster IgG, clone SHG-1) was from BioLegend. These antibodies were labeled in house using AF555 and AF647 labeling kits according to manufacturer’s instructions (ThermoFisher Scientific). Anti-LAMP-1-AF647 clone 1D4B was from BioLegend and anti-early endosome antigen-1 (EEA-1) (#2411) was from Cell Signaling.
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6

Multiplex IHC for EpCAM, α-SMA, and PDGFR-α

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For the simultaneous detection of EpCAM, α-SMA, and PDGFR-α (3164S, 1:200, Cell signaling), fluorescent multiplex IHC involving the tyramide signal amplification methodology was performed using Tyramide SuperBoost™ Kits Alexa Fluor (AF)488, AF555, and AF647 (ThermoFisher). Epitope retrieval was performed in 10 mmol/L sodium citrate (pH 6.0) or 1 mmol/L EDTA (pH 9.0), endogenous peroxidase was inactivated, and the slides were blocked with 10% goat serum prior to primary antibody incubation. The primary antibody was incubated overnight (4 °C) before incubation with AF-conjugated tyramides. Subsequently, same-species primary antibodies were applied after 10 min of the heat-mediated stripping of the antibody complex in citrate buffer and repeating the same procedure above. The slides were counterstained with DAPI and mounted with ProLong® Gold Antifade Mountant (ThermoFisher) and a coverslip before imaging using confocal microscopy (LSM 510 META).
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7

Immunohistochemical Localization of PAC1R and CGRP in BNST

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Every fourth section (120 μm apart) of the BNST region (range, +0.38 to +0.02 mm from bregma) was processed. Free-floating sections were washed in TBS after every incubation. Following initial TBS washes, 10 mm sodium citrate buffer, pH 6, antigen retrieval was performed at 80°C for 30 min. Sections were blocked with a blocking solution (3% normal goat serum in 0.2% Triton X-100 in TBS) for 1 h at RT, followed by incubation with primary antibody [1:250, for 48 h at 4°C; anti-PAC1R; catalog #AVR-003 Alomone Labs (RRID: AB_2756805); 1:250, for 24 h at 4°C; anti-CGRP; catalog #ab81887, Abcam (RRID: AB_1658411)]. Sections were then incubated with secondary antibody (for PAC1R: 1:200; anti-rabbit; catalog #AF555, Thermo Fisher Scientific; for CGRP: anti-mouse; 1:250; catalog #AF488, Thermo Fisher Scientific). Sections were then washed in TBS and coverslipped with DAPI-containing mounting medium (VECTASHIELD Antifade Mounting Medium with DAPI, Vector Laboratories).
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8

Histochemical Analysis of Active MS Lesions

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Frozen brain material from active MS lesions was obtained from The Netherlands Brain Bank. Clinical patient details are depicted in Additional file 1: Table S1. Following acetone fixation (10 min) and blocking (30 min), serial cryosections were stained overnight for proteolipid protein (PLP) to assess demyelination and CD68 or HLA-DR to assess the presence and distribution of microglia/macrophages [30 (link)]. Staining was visualized with HRP-labelled secondary antibodies (Envision+, Dako) and 3,3′-Diaminobenzidine (DAB) substrate-chromogen (Dako). Similarly, sections were stained with antibodies against protein-bound acrolein (1/100, mouse monoclonal, 10A10, Novus Biologicals). For fluorescent double-staining, acrolein-protein adducts were visualized with secondary goat anti-mouse (1/600, AF 555, A-21425, Thermo Fisher), followed by overnight incubation with primary antibodies against CD68 (1/100, mouse monoclonal, M0814 KP1 clone, Dako) or glial fibrillary acidic protein (GFAP, 1/100, mouse monoclonal, G3893, Sigma), and secondary goat anti-mouse (1/400, IgG1 AF 488, A-21121, Thermo Fisher). Imaging was performed with a Leica DM4000 B LED (Leica Microsystems).
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9

Multimarker Immunofluorescence Staining

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The 5 µm tissue cryosections were stained on chipcytometry slides (Zellkraftwerk) with an antibody (polyclonal, AF555, Thermo Fisher Scientific) against the human IgG1-based αTYRP1/αE3 BiAb, a rabbit anti-GFP antibody (polyclonal, Novus Biologicals), a secondary antibody against rabbit IgG (polyclonal, PerCP, Jackson ImmunoResearch) and Hoechst 33 342 (Thermo Fisher Scientific). The fluorescence was measured using the ZellScannerONE (Zellkraftwerk).
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10

c-KIT+ Cell Isolation and Lipid Raft Analysis

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After 4 weeks of the CD or HFD, c-KIT+ cells were isolated with magnetic CD117-Microbeads (Miltenyi Biotec) from BM. Cells were stained with rabbit anti-FLT3 (PA5-34448, Thermo Fisher scientific) and secondary anti-rabbit-AF488 antibodies (Thermo Fisher Scientific). Lipid rafts were stained with cholera toxin subunit B conjugated with AF555 (Thermo Fisher Scientific). Cells were placed on glass slides for 5 min. ProLong Gold Antifade Mountant containing DAPI (Thermo Fisher Scientific) was applied directly to fluorescently labeled cells on microscope slides. Fluorescence was observed by microscopy (Axio Imager 2, Zeiss) and the images were processed (Fiji, NIH).
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