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3 protocols using cell permeabilization buffer

1

Multi-Omics Sample Preparation Protocol

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The following buffers and chemicals were used: erythrocyte lysis buffer (Qiagen, Hilden, Germany), 1 × PBS, made from 10 × PBS (Rockland, Gilbertsville, PA, United States; pH 7.2) using Millipore water, 0.1% cell permeabilization buffer, made from 10 × saponin-based permeabilization buffer (eBioscience), 4% formaldehyde solution in PBS made from 16% paraformaldehyde (EMS, Hatfield, PA, United States), PBS supplemented with 0.5% BSA (PAN Biotech, Aidenbach, Germany), and 0.02% sodium azide (Sigma-Aldrich, St. Louis, MO, United States) (PBS/BSA). Buffers were sterile-filtered through 0.22-μm membranes and stored in Stericup disposable bottles (Merck, Darmstadt, Germany). Blood, urine, and cells were processed in 50-ml, 15-ml, and 5-ml round-bottom polystyrene/polypropylene tubes (Corning, Corning, NY, United States and Sarstedt, Nümbrecht, Germany).
MAXPAR antibody labeling kits, EQ Four element calibration beads, washing and tuning solution, and DNA intercalators were purchased from Fluidigm Corporation (South San Francisco, CA, United States). Pre-conjugated and unlabeled antibodies are summarized in the Supplementary Table S1.
Cis-Platinum (II)-diamine dichloride (cisplatin) was purchased from Enzo Life Sciences GmbH (Lörrach, Germany). A 25 mM stock solution was prepared in DMSO (Sigma-Aldrich) and aliquots were stored at -20°C.
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2

Lung Tissue Digestion and Immune Cell Analysis

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Lungs were perfused with PBS containing EDTA (0.5 mM), minced, and digested in collagenase IV (5 mg/ml) and DNase I (23 (link)). Cells were filtered and washed with RBC lysis buffer (BD Biosciences, Franklin Lakes NJ) and kept on ice in media containing 10% serum. Dead cells were stained with Pac-Orange Live/Dead fixable dead staining dye (Invitrogen). Lung cells were then stained with fluorescent-labeled antibodies against various leukocyte surface markers (CD45, CD11b, CD11c, F4/80, CD103, MHCII, CD86, Clec9a, CD3ε, TCRβ, CD4, CD69, IFN-γ). Appropriate isotype-matched controls were used in all experiments. Antibodies were purchased from EBiosciences (San Diego, CA) or Biolegend (San Diego, CA). Cells were fixed and analyzed on a Canto2 (Becton-Dickinson, San Jose, CA) or FACSAria II (BD Biosciences) flow cytometer. Results were analyzed using FlowJo software (Tree Star, Ashland, OR). For analysis of intracellular IL-12 or IFN-γ, fresh aliquots of digested lung tissue were stimulated for 5 hours at 37°C, with Cell-stimulation Cocktail Buffer (40.5 μmol/L phorbol 12-myristate 13-acetate [PMA], 670 μmol/L ionomycin, 5.3 mmol/L brefeldin A, and 1 mmol/L monensin; eBioscience), fixed, permeabilized with Cell Permeabilization Buffer (eBioscience) and incubated with anti-mouse IL-12 clone C17.8 (eBioscience) or anti-mouse IFN-γ clone XMG1.2 (Biolegend).
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3

Intracellular Flow Cytometry of NKX2-1 and SOX2

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Cells were harvested for intracellular flow cytometry and fixed for 10–20 min at 37°C in fresh 1.6% paraformaldehyde. Cells were permeabilized with Cell Permeabilization Buffer (eBioscience, San Diego, CA) containing 4% normal donkey serum (Sigma) in PBS and stained with primary antibody for NKX2-1 (Abcam rabbit, 1:100) or a conjugated antibody for SOX2 (BD Biosciences, 1:100). Anti-NKX2-1 antibody was detected by secondary antibody staining with either Cy3, Alexa Fluor 488, or Alexa Fluor 647 fluorophore-conjugated secondary antibodies (AffiniPure Donkey Anti-Rabbit IgG (H+L); 1:500; Jackson ImmunoResearch, West Grove, PA). Stained cells were analyzed on a FacsCalibur instrument (BD Biosciences) and data were analyzed with FlowJo software (Ashland, OR).
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