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25 protocols using dapi fluoromount g

1

Quantitative Immunofluorescence Analysis of Liver Infiltration

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The infiltration of inflammatory cells into the liver sections was detected via immunofluorescence staining by applying primary anti-CD11b antibody (ab75476, Abcam), anti-Ly6g antibody (ab25024, Abcam), anti-F4/80 antibody (MCA497, Serotec). After incubation with primary antibody overnight at 4°C, liver sections were incubated with fluorescence-labelled secondary antibodies (Goat anti-rabbit-IgG, A-11011, Thermo Fisher Scientific; Conjugate Anti-rat IgG, 4417, Cell Signalling Technology) for 1 hour. Liver slices were washed and then mounted with DAPI-Fluoromount-G (Thermo Fisher Scientific). Immunofluorescence images were obtained using a fluorescence microscope with DP2-BSW software (version 2.2, Olympus). Positive-staining cells in the images were quantified using Image-Pro Plus software (version 6.0).
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2

Immunofluorescence Staining of FLAG-Tagged Proteins

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HEK293T cells were grown on glass slides for 24 h and transfected as described above. Cells were fixed with 4% paraformaldehyde for 30 min at room temperature and washed three times with ice-cold PBS. The cells were permeabilized and blocked for 1 h at room temperature using 5% donkey serum in PBST (1X PBS, 0.1% Triton X-100). Coverslips were incubated with anti-FLAG mouse primary antibody (1:1000) (Sigma-Aldrich) overnight at 4°C. Coverslips were washed 3x in PBST at room temperature then incubated with fluorescently-labeled secondary antibody (1:2000, Alexa Fluor 488 anti-mouse) for 1 h at room temperature. Coverslips were washed 3x in PBST at room temperature and mounted onto superfrost glass slides using DAPI Fluoromount-G (Thermo Fisher Scientific). Images were visualized using a LEICA SP8 confocal microscope using a 63x objective and analyzed using ImageJ Software (version 2.1.0).
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3

Immunohistochemistry for βIV-spectrin

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Sections were fixed in ice-cold methanol or 4% PFA and blocked in PBS-T and 10% goat serum (1% BSA, 0.2% fish skin gelatin, and 0.1% Triton in 0.1 M PBS for βIV-spectrin staining) for 30 minutes (at least 60 min for βIV-spectrin staining). Primary antibody incubations were carried out overnight at 4°C, and slides were incubated with secondary antibodies for 2 hours. For chromogenic assays, sections were incubated with biotinylated secondary IgG antibodies (Thermo Fisher Scientific, catalog 62-6540, goat anti–mouse IgG [H+L] cross-adsorbed secondary antibody, biotin; 1:500) followed by an avidin-biotin complex for a 1-hour incubation (Vector Laboratories, 1:500) and subsequent color revelation using diaminobenzidine (Dako). H&E staining was carried out for diagnostic purposes. Slides with fluorescent antibodies were mounted with DAPI Fluoromount-G (Thermo Fisher Scientific).
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4

Evaluating Epithelial Barrier Function

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To examine “outside in” physical barrier function, 15 μL Lucifer yellow (LY) (1 mM; ThermoFisher L453) was pipetted to the top of the tissue at days 3 and 14 and incubated at 37°C overnight. Tight junction (TJ) “inside out” function was tested by replacing the medium with 3 mL 1.67 mg/mL biotin tracer (ThermoFisher 21335) on day 14 and incubated overnight. Tissues were fixed in 10% neutral buffered formalin, paraffin embedded, and dewaxed on slides. Biotin tracer slides were subsequently incubated 30 min with 1:200 Alexa Fluor 594 streptavidin (ThermoFisher S11227). Coverslips were mounted with DAPI Fluoromount-G™ (ThermoFisher 00-4959-52).
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5

Immunostaining of Postnatal Mouse Skin Fibroblasts

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Primary fibroblasts isolated from 1–2-day postnatal mouse skin were cultured on eight-well Nunc™ Lab-Tek™ Chamber Slide from Thermo Fischer. The cells were washed two to three times with PBS then fixed and permeabilized using 100% ice-cold methanol. After blocking with 10% normal goat serum, the cells were incubated with primary antibodies overnight at 4°C followed by Alexa Fluor- conjugated secondary antibodies (Life Technologies (Thermo Fisher Scientific) (dilution 1:1000) for 1 h at room temperature. The primary antibodies used were IP3 Receptor 1 (D53A5) (Cell Signaling, 8568S; Lot# 1 dilution 1:200), LAMP2 (Abcam, ab13524; Lot# GR3221693–4; Dilution 1:500), NFATC4 (Abcam, ab62613; Lot# GR70691–12; dilution1:500), LC3B (ab51520; dilution 1:200). Cells were mounted using DAPI-Fluoromount G (Thermo Fisher, 010020) and fluorescence was visualized with the Zeiss LSM 710 Inverted Meta confocal microscope (Carl Zeiss). The images were processed with the LSM Image Software (Carl Zeiss). Mender’s (colocalization coefficient was calculated using the Zen Desk Software from Zeiss.
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6

Detecting ER-Lysosome Contacts in Fibroblasts

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For detection of ER–lysosome contacts, Normal and INCL fibroblasts were seeded on coverslips, fixed and permeabilized with methanol, followed by PLA according to manufacturer’s protocol (SigmaAldrich, Duolink In Situ Detection Reagents) In brief, after permeabilization, the cells were blocked with PLA blocking buffer and incubated with anti IP3R1 (Cell Signaling, 8568S; Lot#1, dilution 1:200) and anti-LAMP2 antibodies (ProteinTech Group, 66301–1-1g, dilution 1:100)—either alone or in combination, for overnight at 4°C, then hybridized with PLA probes; anti-rabbit-MINUS (Sigma-Aldrich; DUO82005 for IP3R1 antibody) and anti-mouse-PLUS (Sigma-Aldrich; DUO82001 for LAMP2 antibody), subjected to ligation and amplification reaction using Duolink Duolink In Situ Detection Reagents Green (Sigma-Aldrich; DUO92014–100RXN) according to the manufacturer’s protocol. The cells were mounted with DAPI-Fluoromount G (Thermo Fisher, 010020) and visualized with Zeiss 710 inverted confocal microscope. The number of PLA puncta were quantified using Image J software.
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7

Immunofluorescence Imaging of Paeoniflorin-Treated Cells

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For immunofluorescence, cells were grown on glass coverslips in 12-well plate. After treatment with indicated concentration paeoniflorin for 24h, the cells were fixed with 4% formaldehyde for 15 minutes at room temperature and washed in PBS for 3×5 minutes. Then 1× Phalloidin-iFluor 488 was added and incubated 90 minutes at RT. After being washed in PBS for 3×5 minutes, coverslips were mounted on glass slides using mounting medium (DAPI Fluoromount-G, Thermo Fisher Scientific, USA). At last, the images were obtained with the Laser Scanning Confocal Microscope (Leica, Germany).
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8

Proximity Ligation Assay for Rab7-RILP Interaction

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Duolink Proximity Ligation Assay38 was used to study interaction between Rab7 and RILP. Briefly the primary neurons from WT and Cln1−/− mice were grown in chamber slides and fixed with methanol for 15 to 20 min at −20°C. The cells were blocked with goat serum and incubated with Rab7 antibody (Abcam; Cat#ab50533; dilution 1:1000) and RILP antibody (Abcam; Cat#ab140188; dilution 1: 3000) overnight at 4°C. After three washes with PBS the cells were incubated with anti-rabbit-MINUS (Sigma–Aldrich; Cat#DUO92005 Anti-RILP) and anti-mouse–PLUS (Sigma–Aldrich; Cat#DUO92001-for Rab7 antibody) PLA probes and subjected to ligation and amplification reaction using Duolink® In Situ Detection Reagents Green (Sigma–Aldrich; DUO9201) according to manufacturer’s protocol. For controls, cells were similarly processed but without primary antibody or with one primary antibody only. When the primary antibodies were in close proximity (<40 nm apart) fluorescent signals were detected as green dots under the FITC channel. The cells were mounted with DAPI-Fluoromount G (Thermo Fisher, Cat#010020) and visualized using an LSM710 confocal microscope. High resolution z stack images were captured at 40X, the z stacks were merged by maximum intensity projection using Zen Desk software to include all the PLA signals and quantitated using Duolink image tool.
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9

Immunocytochemical Staining of HaCaT Cells

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Immunocytochemical staining was performed as in our previous study (10 (link)). Briefly, HaCaT cells were plated on Nunc Lab-Tek Chamber Slides (cat. no. 177429; Thermo Fisher Scientific Inc.) and cultured with or without TGF-β1 for 48 h at 37˚C with 5% CO2. The cells were fixed with 4% paraformaldehyde in PBS for 20 min at 21-25˚C, permeabilized with 0.1% Triton X-100 in PBS for 3 min, and then washed 3 times with PBS. Staining of filamentous actin (F-actin) was achieved by blocking with 1% BSA in PBS for 30 min at 21-25˚C, followed by probing with Alexa Fluor 488 Phalloidin (1:50; cat. no. A-12379; Thermo Fisher Scientific, Inc.) for 1 h at 21-25˚C. Staining of SNAI2 was carried out by probing first with an anti-Slug (1:100; cat. no. 9585; Cell Signaling Technology, Inc.) for 2 h at 21-25˚C and then anti-rabbit IgG antibody conjugated with Alexa Fluor 488 (1:800; cat. no. A-11008; Thermo Fisher Scientific, Inc.) for 1.5 h at 21-25˚C. After staining, DAPI Fluoromount-G® (cat. no. 0100-20; SouthernBiotech) was used to visualize nuclei and preserve fluorescence. Finally, fluorescent images were captured by a fluorescence microscope (BZ-9000; Keyence Corporation; magnification, x200).
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10

Immunofluorescence Imaging of Cell-ECM Interactions

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Cells were grown to 40% confluence in 8-well glass chamber slides (Nunc, Thermo Fisher Scientific), prior to growth arrest and treatment. Cells were washed with PBS before fixation in 4% paraformaldehyde for 10 min at room temperature. Next, cells were permeabilized with 0.1% (v/v) Triton X-100 in PBS for 10 min at room temperature. For visualization of ECM, cells were fixed with 100% ice-cold methanol for 8 min at −20 °C. Slides were washed with PBS and blocked with 1% goat serum (TBD Science, Tianjin, China) for 30 min before washing with 0.1% (w/v) BSA in PBS. Subsequently, slides were incubated with monoclonal mouse anti-α-SMA antibody (Sigma-Aldrich, 1:50) diluted in 0.1% BSA-PBS, overnight at 4 °C. After further wash steps, slides were incubated with goat anti-mouse IgG CF-488 secondary antibody (Abcam, 1:1000) in 0.1% BSA-PBS for 1 h at room temperature and under darkness. For F-actin visualization, after fixation and permeabilization; cells were incubated with phalloidin conjugated to FITC (Sigma-Aldrich) in 0.1% BSA-PBS, overnight at 4 °C. Cells were then mounted in DAPI Fluoromount-G (Thermo Fisher Scientific) and imaged using a Zeiss Axio Imager Z1 UV fluorescence microscope (Zeiss, Jena, Germany) and a Leica TCS SP5 laser scanning confocal microscope (Leica Biosystems, Baden-Württemberg, Germany).
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