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6 protocols using four well culture slides

1

Immunofluorescence Staining for Vimentin and Ki-67

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Cells (1 × 104) growing in four-well culture slides (BD Falcon, Bedford, MA) were fixed with ice cold methanol. For permeabilization, 0.1% Triton X-100 was added to cells for 10 min. To block nonspecific antibody binding, cells were incubated in 1% BSA (Sigma-Aldrich), 0.3 M glycine in PBST buffer (PBS with 0.1% Tween 20) for 30 min at RT. Next, cells were incubated with anti-vimentin and anti-Ki-67 antibodies for 40 min at RT. For visualization FITC-conjugated and Alexa Fluor® 594-conjugated secondary antibodies were used for 1 h at RT. Stained cells were visualized using an Axioscop 2 PLUS fluorescence microscope (Carl Zeiss, GmbH).
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2

Visualizing Autophagy via LC3 Staining

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Cells (1×104) were cultured in four-well culture slides (BD Falcon, Bedford, MA) and treated with RL2 (200 μg/mL) for 8 hours. Cells were fixed with 4% paraformaldehyde and incubated with primary antibody against LC3 (1 μg/mL) for 20 min, followed by FITC-conjugated secondary antibody (1∶1000). Primary and secondary antibodies were diluted in blocking solution (PBS supplemented with 0.05% Tween 20 and 1% gelatin). Stained cells were visualized under an Axioscop 2 PLUS fluorescence microscope (Carl Zeiss, GmbH).
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3

Immunofluorescent Analysis of Stem Cell Markers

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Cells growing in four-well culture slides (BD Falcon, Bedford, MA) were fixed in 4% paraformaldehyde for 10 min. For permeabilization, 0.1% Triton X-100 was added to the cells for 10 min, then, they were incubated in 5% goat serum in PBS for 30 min at RT to block nonspecific antibody binding. Next, the cells were incubated with Sox-2 (Abcam, Cambridge, MA), Oct-4 (Abcam, Cambridge, MA), c-Myc (Abcam, Cambridge, MA), CD133 (Proteintech, USA), and ABCG2 (Abcam, Cambridge, MA) primary antibodies overnight at 4°C. Secondary antibody staining was performed with either IgG/TRITC goat antirabbit or IgG/TRITC goat antimouse antibody at a 1 : 300 dilution for 2 h at room temperature. Images were captured under a fluorescence microscope (Zeiss Axiovert 200M).
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4

Immunofluorescence Staining of Cell Markers

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Cells (1  ×  104) growing in four-well culture slides (BD Falcon, Bedford, MA) were washed with PBS and 10% neutral-buffered formalin. To block nonspecific antibody binding, cells were incubated in 1% BSA (Sigma-Aldrich, Burlington, MA, USA) and 0.3 M glycine in PBST buffer (PBS with 0.1% Tween 20) for 30 min at RT. Next, cells were incubated with the VIMENTIN (#ab8069, Abcam, Cambridge, UK) and E-CADHERIN (#2220530, Sony Biotechnology Inc., San Jose, CA, USA), S100A4 (#MA5-31333, Invitrogen, Waltham, MA, USA) and αSMA (#ab5694, Abcam, Cambridge, UK) antibodies for 60 min at RT. For visualization, FITC-conjugated (#ab97050, Abcam, Cambridge, UK) or Alexa Fluor 555-conjugated (#A32727, Invitrogen, Waltham, MA, USA) secondary antibodies were used for 1 h at RT. Stained cells were visualized using an Axioscop 2 PLUS fluorescence microscope (Carl Zeiss, GmbH, Jena, Germany) or inverted microscope (Eclipse Ti, Nikon, Tokio, Japan).
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5

Immunofluorescence Staining of Cultured Cells

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Cells (5 × 104 each well) were seeded on four-well culture slides (Becton Dickinson Labware, Franklin Lakes, NJ, USA). After 24 h, slides were washed in PBS, fixed with 4% paraformaldehyde for 30 min and non-specific binding was blocked using 1% BSA/PBS. Slides were then incubated with an anti-c-Jun antibody (1:40; Santa Cruz Biotechnology, Heidelberg, Germany) or anti-TUB1 antibody (1:500; Sigma-Aldrich, Steinheim, Germany), washed three times with PBS, and incubated with the AlexaFlour-anti-rabbit or AlexaFlour-anti-mouse antibody (1:150; Invitrogen, Groningen, The Netherlands). Afterwards, they were washed again and finally sealed with VectaShield mounting medium (Vector Laboratories, Burlingame, CA, USA) including 1 mg/mL DAPI (Sigma-Aldrich, St. Louis, MO, USA). Images were collected by fluorescence microscopy or confocal microscopy.
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6

Subcellular Localization of Inflammasome Proteins

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Cells were grown to near confluency in four well culture slides (Becton Dickinson, Franklin Lakes, NJ) and exposed to either asbestos or CNT for 24 hours with or without pre-treatment of cyto D. Cells were fixed in 4% paraformaldehyde (PFA) for 10 minutes followed by permeabilization with 0.1% Triton-X for 10 minutes at room temperature (RT). Auto fluorescence was blocked with 0.3M glycine and non-specific antibody binding was blocked with 20% goat serum in 1x PBS for 1 hour. Cells were incubated with either anti-rabbit ASC or NLRP3 (Novus Biologicals, Littleton, CO) combined with either mitochondrial marker anti-mouse PRDX3 (AB Nova, Walnut, CA) or ER marker anti-mouse calnexin (Novus Biologicals) diluted 1:50 in 1% BSA/PBS overnight at 4°C in a humidified chamber. The following day, a mixture of secondary antibodies Alexa Fluor® 647 goat anti-rabbit and Alexa Fluor® 568 goat anti-mouse (Life Technologies, Grand Island, NY ) diluted 1:400 in 1xPBS were applied to cells for 1 hour at RT. The nuclear stain DAPI (Life Technologies) was diluted 1:200 and added to cells for 20 minutes at RT. Slides were then mounted and coverslipped with Aqua-Poly/Mount (Polysciences Inc., Warrington, PA) and stored at 4°C. Confocal images were acquired using a Zeiss 510 META laser scanning confocal microscope (Carl Zeiss, Thornwood, NY).
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