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14 protocols using 4 6 diamidino 2 phenylindole dapi dye

1

Ferroptosis Inducers and Inhibitors

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Penicillin, trypsin‐EDTA, streptomycin, and dimethyl sulfoxide (DMSO) were obtained from Sigma‐Aldrich (St. Louis, MO, USA). RIPA lysis buffer and bovine serum albumin (BSA) were purchased from Beyotime (Shanghai, China). Protease inhibitor cocktail, phosphatase inhibitor cocktail, 4’,6‐diamidino‐2‐phenylindole (DAPI) dye, and trypsin‐EDTA were acquired from Thermo Fisher Scientific (Scoresby, Vic, Australia). Minimum essential medium α (α‐MEM) and foetal bovine serum (FBS) were acquired from Gibco (Grand Island, NY, USA). Ferrostatin‐1 (MF: C15H22N2O2, MW: 262.35), RSL3 (MF: C23H21CIN2O5, MF: 440.88) and Oltipraz (MF: C8H6N2S3, MW: 226.34) were purchased from MedChem Express (Shanghai, China).
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2

Visualizing Inducible Protein Expression in HeLa Cells

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HeLa or HeLa HF1–3 cells expressing GFP or A3′SS-T2-CP were grown on glass coverslips for 24 h and transfected with 300 ng TetR-mCherry plasmid using 2 µL of Lipofectamine 2000 (Life Technologies) according to manufacturer instructions. Two hours after transfection, the medium was changed to DMEM with or without 50 µM doxycycline and further incubated at 37°C and 5% CO2 for 24 h. Next, cells were fixed in 3.7% formaldehyde at room temperature (RT) for 10 min followed by permeabilization with 0.5% triton X-100 in 1×PBS for 10 min at RT. Cells were then washed three times with 1× PBS and stained with 4′,6-diamidino-2-phenylindole (DAPI) dye (1 µg/mL in water; Thermo Scientific) and washed three times with 1x PBS. Finally, coverslips were mounted with mounting medium (Thermo Scientific). All experiments were carried out on a Zeiss Axiovert 200 M inverted microscope using a 63×/1.4 NA oil objective lens (Zeiss). Excitation was done using the mercury arc lamp (Zeiss). The following filters were used: 350/50 (excitation) and 460/50 (emission) for DAPI, 482/18 (excitation) and 520/28 (emission) for GFP, and 565/30 (excitation) and 620/60 (emission) for mCherry. Images were repeated three times. Data processing was performed using ImageJ.
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3

Doxorubicin-Loaded PLGA Nanoparticles

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Doxorubicin, (7S, 9S)-7-[(2R, 4S, 5S, 6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyacetyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione), was a gift sample from Sun Pharmaceutical, Gujrat, India. PLGA {poly (lactide-co-glycolide) ratio 85:15, MW 50,000–75,000} was procured from Sigma-Aldrich Co, St Louis, MO, USA. Polyvinyl alcohol was purchased from SD Fine-Chemicals limited, Mumbai, India. Dimethylsulfoxide (DMSO) and dichloromethane (DCM) were procured from Merck Life Science Pvt. Ltd, Bengaluru, India. Pluronic F-68 was purchased from Himedia Laboratories Pvt. Ltd. Mumbai, India. Tween 80 was procured from SD Fine-Chemicals limited, Mumbai, India, D-α-Tocopherol polyethylene glycol succinate (TPGS), Pluronic F127 and Suberic acid bis (3-sulfo-N-hydroxy succinimide ester) (BS3) were purchased from Sigma-Aldrich Co, St Louis, MO, USA. FITC anti-human CD-340 (erb B2/HER-2) was purchased from Biolegend, San Diego, California, United States. The media were procured from Himedia Laboratories Pvt. Ltd. Mumbai, India. 4',6' diamidino-2-phenylindole (DAPI) dye was procured from Thermo Fisher Scientific, Waltham, MA USA.
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4

Immunofluorescence Staining of Liver Cancer Cells

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Hep3B and Huh1 cells were seeded onto Poly-lysine (P4707, Millipore Sigma, Darmstadt, Germany) coated cover glasses. 1–2 days later, cells were washed with PBS three times at room temperature and then fixed with 4% paraformaldehyde Fix Solution (Cat: E672002, Sangon, Shanghai, China) for 15 min. Next, the fixed cells were permeabilized with 0.2% Triton X-100 (Cat: E-IR-R122, Elabscience Biotechnology, Wuhan, China) for 10 min at room temperature. Sections were incubated with Ki67 (Cat: 27,309–1-AP, Proteintech, Rosemont, USA) or β-catenin (Cat: #8480, CST) primary antibodies at 4ºC overnight. The next day, sections were washed using PBS for 3 × 5 min at room temperature, and then incubated with 4',6-diamidino-2-phenylindole (DAPI) dye (Cat: D1306, ThermoFisher Scientific, Waltham, MA, USA) and fluorophore-conjugated secondary antibodies at room temperature for 2 h. Images were captured by the Leica microscope.
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5

Immunofluorescence Assay for γH2AX

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Cells were seeded onto Poly-lysine (cat: P4707, Millipore Sigma, Darmstadt, Germany) coated cover glasses. 1–2 days later, cells were washed with PBS three times at room temperature and then fixed with 4% paraformaldehyde Fix Solution (cat: E672002, Sangon, Shanghai, China) for 15 min. Next, the fixed cells were permeabilized with 0.2% Triton X-100 (cat: E-IR-R122, Elabscience Biotechnology, Wuhan, China) for 10 min at room temperature. Sections were incubated with γH2AX (cat: ab26350, Abcam Cambridge Science Park, Cambridge, UK) primary antibodies at 4°C overnight. The next day, sections were washed using PBS for 3 × 5 min at room temperature, and then incubated with 4’,6-diamidino-2-phenylindole (DAPI) dye (cat: D1306, ThermoFisher Scientific, Waltham, MA, USA) and fluorophore-conjugated secondary antibodies at room temperature for 2 h. Images were captured by the Leica microscope.
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6

Quantifying Bacterial Counts in Water Samples

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The concentration of monochloramine in water samples was measured using a portable colorimeter (DR900, Hach, Loveland, CO, USA) with monochlor F reagent pillows. A pH meter (SK-620PH, Sato Keiryoki Mfg. Co., Tokyo, Japan) was used to measure the pH of the FS. Surface images of the FO membrane were attained using a scanning electron microscope (SEM) (Tabletop Microscope TM3030Plus, Hitachi High-Technologies, Tokyo, Japan). Bacterial counts in feed solutions were determined using a fluorescence microscope (Shibasaki, Inc., Chichibu, Japan). Each sample was first diluted 200–20,000 times using microfiltration (MF) membrane-treated pure water. Thereafter, 1 mL of the diluted sample was filtered using a track-etched polycarbonate MF membrane with a 0.2 µm pore size (Meric, Tokyo, Japan). After staining, the bacterial number deposited on 40% of the filter surface area was measured. Total bacterial counts (both viable and nonviable bacteria) were measured by staining with 4′-6-diamidino-2-phenylindole (DAPI) dye (Thermo Fisher Scientific, Waltham, MA, USA). Viable bacterial counts were calculated by deducting counts of dead (inactivated) bacteria determined by staining with 3,6-bis(dimethylamino)acridine hydrochloride solution (Dojindo Laboratories, Kumamoto, Japan) from total bacterial counts.
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7

Wnt5a and ROR1 expression in CLL cells

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CLL cells were fixed in 2% paraformaldehyde for 10 minutes at 37°C and permeabilized overnight at −20°C. Before staining, cells were washed three times in PBS with 2% fetal bovine serum (FBS; Invitrogen). Then, the cells were incubated in micro tubes in PBS supplemented with 5% FBS. After 1 hour of incubation, the cells were washed three times with PBS and then incubated with rabbit anti-Wnt5a antibodies (Invitrogen) and mouse anti-ROR1 antibodies (Invitrogen) for 1 hour. After being washed three times with phosphate-buffered saline, the cells were incubated with Alexa flour 488 labeled anti-rabbit and Alexaflour 647 labeled anti-mouse antibodies. After being washed three times with PBS, the cells were suspended in 5 mg/ml solution of 4’,6-diamidino-2-phenylindole (DAPI) dye (Invitrogen) for 15 minutes and then washed in PBS to remove the unbound dye. The cells were then placed into μ-slide VI chamber slides (ibidi, LLC) for microscopic analysis. The slides were viewed using an Olympus FluoView 500 confocal laser scanning microscope (Olympus America, Waltham, MA), and images were analyzed using the FluoView software (Olympus America).
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8

Synthesis and Characterization of Multimodal Nanosystem

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Polyacrylic acid (PAA), 2-morpholinoethanesulfonic acid (MES), 1-ethyl-3-(3-dimethylaminopropylcarbodiimide hydrochloride (EDC), propargylamine (PA), N,N’-dimethyl sulfoxide (DMSO), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), chloropropylamine and N,N’-dimethylformamide (DMF) were purchased from Sigma-Aldrich and used as received. Near infra-red DiI dye and 4, 6-diamidino-2-phenylindole (DAPI) dye were purchased from Invitrogen. Cerium nitrate hexahydrate, N-hydroxy succinimide (NHS), tetrahydrofuran, acetonitrile, sodium azide, ammonium hydroxide, ethanol, folic acid, isopropanol, and MES sodium salt were purchased from ACROS organics and used without further purification. Dialysis membranes were received from spectrum laboratories. Dihydroethidium (DHE) was obtained from Cayman chemical, whereas H2O2 and para-formaldehyde received from electron microscopy sciences. Fetal bovine serum (FBS), 5× Annexin V binding buffer purchased from BD Biosciences, whereas ganetespib, isopropyl alcohol, apoptosis and necrosis quantification kit (FITC-Annexin V, Ethidium homodimer III) were obtained from Biotium. Migration assay kit was purchased from Millipore. Rat cardiomyocytes (H9c2 cells), A549 cells (NSCLC), DMEM and F12K cell culture media were purchased from ATCC, USA.
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9

Paeonol-Based Antimicrobial Assessments

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Paeonol (purity ≥98%) was purchased from Chengdu Pulis Biological Science and Technology Co. Ltd. (Chengdu, China). Stock solutions of paeonol were dissolved in ddH2O at final concentrations of 5 mg ml−1 and kept at −20°C. SYTO 9, FUN® 1, Calcofluor® White M2R stain (CWS), Film Tracer SYPRO Ruby (SYPRO Ruby), wheat germ agglutinin (WGA), propidium iodide (PI), and 4′,6-diamidino-2-phenylindole (DAPI) dye were purchased from Invitrogen (Thermo Fisher Scientific, Waltham, Massachusetts, USA). Gatifloxacin was obtained from Shanghai Yuanye Bio-Technology Co. Ltd. (Shanghai, China). Other chemicals used were of analytical grade or better.
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10

Immunofluorescence Analysis of CLL Cells

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CLL cells were incubated in microtubes with phosphate-buffered saline (PBS) supplemented with 2% bovine serum (HyClone) and with anti–S6 ribosomal protein antibodies (Cell Signaling Technology) and anti-CD5 antibodies (Becton, Dickinson and Company) for 1 hour. After being washed three times with phosphate-buffered saline, the cells were suspended in 5 mg/ml solution of 4′,6-diamidino-2-phenylindole (DAPI) dye (Invitrogen) for 5 minutes and then washed in phosphate-buffered saline to remove the unbound dye. The cells were then placed into μ-slide VI0.4 chamber slides (ibidi, LLC) for microscopic analysis. The slides were viewed using an Olympus FluoView 500 confocal laser scanning microscope (Olympus America), and images were analyzed using the FluoView software (Olympus America).
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