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49 protocols using acrylamide bis solution

1

Reagents and Chemicals for Cell Culture Studies

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Fetal Bovine Serum (FBS) and Phosphate Buffered Saline (PBS) were purchased from Hyclone™, ThermoFisher Scientific, Waltham, MA, USA. HEPES, EDTA, EGTA, TEMED, isopropanol, aprotonin, pepstatin, phenylmethanesulfonyl fluoride (PMSF), leupeptin, sodium fluoride (NaF), sodium orthovanadate (Na3VO4), diethyldithiocarbamate (DDC), doxorubicin, etoposide, fludarabine, 5-flouroUracil (5-FU), cisplatin, dimethyl-9,9’-biacridinium dinitrate (Lucigenin), N-acetyl-cysteine (NAC) were purchased from Sigma-Aldrich, St. Louis, MO, USA. Venetoclax (VEN) was purchased from Medchem Express LLC. Streptomycin–penicillin and l-glutamine were purchased from Gibco. Coomassie Blue dye and bovine serum albumins (BSA) were purchased from ThermoFisher Scientific. Methanol and sodium dodecyl sulphate (SDS) were purchased from Merck, Kenilworth, NJ, USA. Sucrose and 30% acrylamide/bis solution were purchased from Bio-Rad. Goat anti-mouse and anti-rabbit IgG horseradish peroxidase conjugated secondary antibodies were purchased from Pierce, TX, USA. Protein A agarose beads were purchased from Santa Cruz, TX, USA. Chloromethyl-2-,7-dichlorofluorescin diacetate (DCFDA) and MitoSox™ were purchased from Molecular Probes, Thermo Fisher Scientific.
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2

Quantitative Western Blot Analysis

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Cells were lysed in sample buffer (2% SDS, 0.1 mg/ml bromophenol blue, Tris-HCl pH 6.8, 5% 2-mercaptoethanol and 10% glycerol), and boiled at 100°C for 5 min. For the one of experimental group, each cells of 6-well plate were recovered with 200 μl sample buffer and accumulate. Protein was quantified using the bicinchoninic acid (BCA) (Thermo Scientific) assay after addition of sample buffer. The samples were loaded on 10% SDS-polyacrylamide gel electrophoresis (3.3 ml of 30% acrylamide/Bis Solution (BIO-RAD, CA, USA), 2.5 ml of 1.5 M Tris Glycine buffer (pH 8.8, Dyne Bio, Korea, Gyeonggi-do), 0.1 ml of 10% SDS solution (Dyne Bio, Korea, Gyeonggi-do), 0.1 ml of 10% ammonium persulfate solution (Dyne Bio, Korea, Gyeonggi-do), 4 ul of N,N,N’,N’-Tetramethylethylenediamine (Biosesang, Korea, Gyeonggi-do) and 4.0 ml of H2O), then the separated proteins were transferred to a nitrocellulose membrane (BIO-RAD, CA, USA), and then incubated with primary antibodies recognizing β-actin (Sigma–Aldrich, St Louis, USA), type I collagen, fibronectin, β-catenin, wnt3a and interleukin-1α (IL-1α) (ABCAm, Massachusetts, USA). Protein detection was performed with Lumi Femto (Daeil Laboratory Service, Seoul, Korea) and the Molecular Imager ChemiDoc XRS+ station. Image J software (National Institutes of Health, Bethesda, MD, USA) was used to analyze and quantify the western blot image.
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3

Oxidative Stress Regulation in Endothelial Cells

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Gelatin, Heparin, 2’,7’-Dichlorofluorescein diacetate (DCF-DA), Dihydroethidum (DHE), Protoporphrin IX cobalt chloride (CoPPIX), RIPA buffer and Thiazolyl blue tetrazolium (MTT) were obtained from Sigma-Aldrich (St. Louis, MO). Endothelial Cell Growth Supplement (ECGS) was purchased from Fisher Scientific (Pittsburgh, PA). MCDB131, RPMI-1640, Lipofectamine™ 2000, L-Glu, trypsin, Dulbecco's phosphate buffered saline 1X and penicillin-streptomycin were purchased from Invitrogen (Carlsbad, CA). Sodium pyruvate was obtained from Irvine Scientific (Santa Ana, CA). Fetal Bovine Serum (FBS) was from Hyclone (Logan, UT). Tin Protoporphrin IX dichloride (SnPPIX) was obtained from Tocris Bioscience (Elisville, MO). Ammonium Persulfate, 2-Mercaptoethanol, N,N,N’,N’-tretra-methyl-ethylenediamine (TEMED), Laemmli Sample buffer, 30% Acrylamide/Bis Solution and Protein Dye Reagent Concentrate were purchased from Bio-Rad (Hercules, CA). HO-1 mouse monoclonal and Goat anti-mouse antibody-HRP conjugate antibody were purchased from Assay designs (Ann Arbor, MI). GAPDH rabbit polyclonal antibody and Goat anti-rabbit antibody-HRP conjugate antibody were purchased from Santa Cruz Biotechnology. ECL Plus Western Blotting Detection System was obtained from GE Healthcare (Buckinghamshire, UK).
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4

Characterization of Remicade® Binding to Lipid Bilayers

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1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phosphorylglycerol sodium salt (DMPG) were purchased from Avanti Polar Lipid Inc. (Alabaster, AL, USA). Cholesterol (Chol), α-tocopherol, bovine serum albumin (BSA) fluorescein isothiocyanate conjugate (FITC-BSA), ammonium persulfate, pepsin, pancreatin, and Remicade® (IFX) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Cy™7 Mono NHS Ester was purchased from GE Healthcare (Little Chalfont, Buckinghamshire, UK). BCA Protein Assay Kit and PageRuler Prestained Protein Ladders were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Sodium dodecyl sulfate (SDS) was purchased from Kracker Scientific (NY, USA). Coomassie-brilliant blue R-250 staining solution, 30% acrylamide/Bis solution (29:1), TEMED, 4 × Laemmli sample buffer, 1.5 M Tris–HCl buffer and 0.5 M Tris–HCl buffer were purchased from Bio-Rad Laboratories (Hercules, CA, USA.). Magnesium chloride hexahydrate (98%) and other inorganic salts were purchased from Junsei Chemical Co. (Tokyo, Japan). Eudragit® S100 was kindly donated by Evonik Korea (Seoul, Korea).
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5

Antioxidant Compound Analysis Protocol

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Morin hydrate and resveratrol were purchased from Tokyo Chemical Industry (TCI) (Tokyo, Japan). Quercetin, Folin–Ciocalteu solution, 2,20-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS), 1,1-diphenyl-2-picrylhydrazyl (DPPH), and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Ferric chloride, ferrous sulfate, sodium carbonate, sodium acetate, aluminum trichloride, and potassium persulfate were purchased from Merck (Darmstadt, Germany). Dulbecco’s modified Eagle’s medium (DMEM), RPMI-1640 medium, and penicillin–streptomycin were purchased from GIBCO Invitrogen™ (Grand Island, NY, USA). Fetal bovine serum (FBS) was obtained from Biochrom AG (Berlin, Germany). Protein markers, 0.5 M Tris–HCl, pH 6.8 solution, 1 M Tris–HCl, pH 8 solution, and 30% acrylamide/bis solution, were purchased from Bio-Rad Laboratories (Richmond, CA, USA). Ethanol, n-hexane, ethyl acetate, and dimethyl sulfoxide (DMSO) were purchased from Labscan (Dublin, Ireland). HPLC grade Ethanol was purchased from Carlo Erba Reagents (Cornaredo, Italy).
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6

Immunofluorescence Analysis of TSSK3 in Cells

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Reagents were obtained from various sources and details are provided below, under the subsections pertaining to each experimental procedure. Bovine serum albumin (A-7906, for blocking non-specific binding), Tween-20 (P-7949), Immobilon-P PVDF membrane (Millipore) and poly-L-lysine (P-8920) were purchased from Sigma-Aldrich (St. Louis, MO). Paraformaldehyde (16% solution, EM Grade), and β-mercaptoethanol were purchased from Fisher Scientific (Waltham, MA). Triton X-100 and 30% acrylamide/Bis solution were obtained from BioRad. Peroxidase-conjugated anti-mouse IgG (Jackson Immunoresearch, West Grove, PA) and peroxidase-conjugated anti-rabbit IgG (GE Healthcare, Pittsburg, PA) were used. AlexaFluor488-conjugated PNA lectin, AlexaFluor488-conjugated anti-rabbit IgG, Hoechst 333452 and gentamicin (10 mg/ml) were purchased from Invitrogen (ThermoFisher Scientific, Grand Island, NY). Anti-TSSK3 rabbit polyclonal antibodies AP7246a and AP17810b were obtained from Abcepta (San Diego, CA). A rabbit polyclonal antibody against alpha/beta-tubulin was obtained from Cell Signaling Technology (Danvers, MA).
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7

Establishment of EV71 C4a Virus Protocol

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EV71 C4a, the non-mouse adapted EV71 strain, Fuyang.Anhui.P.R.C/17.08/3 (GenBank: EU703814.1), was generously gifted by HK inno.N corp (Seoul, South Korea) for basic research [24 (link)]. Vero cell-line (Vero African green monkey kidney cells) was purchased from Korean Cell Line Bank (Seoul, South Korea). AddaVax® was purchased from Invivogen (San Diego, CA, USA). Kanamycin was purchased from Sigma-Aldrich (St. Louis, MO, USA). Luria-Bertani (LB) broth, Bacto® Agar (BD Difco, NJ, USA), and isopropyl-β-D-1-thiogalactopyranoside (IPTG) were purchased from Bioneer (Daejeon, South Korea). D-Plus™ Protein Gel Staining Solution was purchased from Dongin Biotech Co. (Seoul, South Korea). The Polyvinylidene fluoride (PVDF) membrane, ammonium persulfate, 10% sodium dodecyl sulfate (SDS) solution, and 30% acrylamide/bis solution were purchased from Bio-Rad (Hercules, CA, USA). Horseradish peroxidase (HRP)-conjugated rabbit anti-mouse IgG and IgG1 antibodies were purchased from Abcam (Cambridge, MA, USA.) and Southern Biotech (Birmingham, AL, USA), respectively. Pierce TMB substrate kits, HIS-bind® purification resin, and sulforhodamine B (SRB) were purchased from Thermo Fisher Scientific (Waltham, MA, USA).
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8

Recombinant FXIII-A2 and Thrombin Activity

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Recombinant human FXIII-A2 was obtained from the late Dr. Paul Bishop (Zymogenetics, Seattle, WA), and recombinant human thrombin from E. Di Cera and L. Pelc (St. Louis University, MO). The activity of the recombinant human thrombin was determined using titration against hirudin.31 (link) Human plasma fibronectin and Phe-Pro-Arg-chloromethyl ketone (PPACK) were supplied by Haematologic Technologies (Essex Junction, VT, USA). Bovine thrombin, human α2-antiplasmin, actin, ferulic acid, α-cyano-4-hydroxycinnamic acid (α-CHCA), N,N-Dimethyl-p-phenylenediamine (DMPDA), monodansylcadaverine (MDC), and Glycine ethyl ester (GEE) hydrochloride were obtained from Millipore Sigma (St. Louis, MO, USA). Peptides α2AP WT (1 – 15) and α2AP Q4S (1 – 15) were synthesized by New England Peptide (Gardner, MA, USA). Peptide stock concentrations were determined by quantitative amino acid analysis (AAA Service Laboratory, Damascus, OR, USA). Sequencing grade chymotrypsin and GluC endoproteinase, both from Roche, were supplied by Millipore Sigma (St. Louis, MO, USA). 30% Acrylamide/Bis solution, 4 – 20 % precast tris-glycine gels, and dual-color molecular weight standards were purchased from Bio-Rad Laboratories (Richmond, CA, USA).
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9

Investigating Apoptosis Signaling Pathways

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We used commercial ECM (Matrigel; Collaborative Research) for the rBM assays. Primary antibodies used were as follows: cleaved caspase 3 (1:400, 9661; Cell Signaling Technology), phospho-c-Jun (serine 63; 1:1,000, 3270; Cell Signaling Technology), JNK1/JNK2 (1:1,000, 554285; BD PharMingen), E-cadherin (1:1,000, 3195; Cell Signaling Technology), phospho-JNK (G-7) mAb (1:100, sc-6254; Santa Cruz Biotechnology), HA.11 clone 16B12 (1:2,000; BabCo), and p65 (1:1,000 Western blot, 1:800 IHC, 8242; Cell Signaling Technology). The secondary antibodies used were as follows: HRP-conjugated anti-rabbit and anti-mouse (Amersham Biosciences) and Alexa Fluor 488– and Alexa Fluor 555–conjugated anti-mouse and anti-rabbit IgGs (Molecular Probes). The following reagents were used in these studies: PI, DAPI, MTT, and Weigert’s iron hematoxylin (all from Sigma-Aldrich); N-tetramethyl ethylenediamine, 30% acrylamide/bis solution (37.5:1; 2.6% C), 40% acrylamide solution, and 2% bis solution (Bio-Rad Laboratories); TRAIL (100–200 ng/ml), paclitaxel (5–100 nM), and the JNK inhibitor SP600125 (5 µM, A4604; APExBIO); recombinant human TNFα (20 ng/ml, 68-8786-63; Invitrogen); and NF-κB inhibitor JSH-23 (481408; MilliporeSigma).
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10

Purity Verification and Cell Culture Protocol

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PF (purity > 98%) was purchased from Cayman Chemical Co. (Ann Arbor, MI, USA). For cell culture, fetal bovine serum (FBS), Dulbecco's modified Eagle's medium (DMEM), and penicillin/streptomycin were obtained from Welgene (Daegu, Korea). Griess reagent, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), and dimethyl sulfoxide (DMSO) were supplied by Sigma Chemical Co. (St. Louis, MO, USA). Radioimmunoprecipitation assay (RIPA) buffer, 30% acrylamide bis solution, and pre-stained protein size markers were obtained from Bio-Rad (Hercules, CA, USA). Polyvinylidene fluoride (PVDF) membrane was obtained from Millipore (Billerica, MA, USA). Prior to use, PF was freshly prepared as a stock solution in DMSO.
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