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10 protocols using acrylamide

1

Proteomics Sample Preparation

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Acrylamide, bisAcrylamide, Dithiothreitol (DTT), iodoacetamide, 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), Sodium Dodecyl Sulfate (SDS), urea, glycerol, thiourea, Tetramethylethylenediamine (TEMED), Ammonium Persulfate (APS), molecular markers and Immobilized pH Gradient (IPG) buffer were obtained from GE Healthcare Life Sciences (São Paulo, SP, Brazil). Triton X-100, Bovine Serum Albumin (BSA) and Coomassie Brilliant Blue (CBB) were obtained from Sigma-Aldrich (São Paulo, SP, Brazil). Trypsin was obtained from Promega (São Paulo, SP, Brazil).
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2

Two-Dimensional Gel Electrophoresis Reagents

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Acetonitrile (ACN), acetone, trifluoroacetic acid (TFA), trichloroacetic acid (TCA), DL-dithiothreitol (DTT), iodoacetamide (IAA), glycine, EDTA, Tris, endonuclease, phosphoprotease and protease inhibitors, lanthanum chloride, potassium dihydrogen phosphate, Coomassie Blue G-250 were purchased from Sigma (Sigma-Aldrich, St. Louis, MO, USA); urea, CHAPS, SDS, glycerol, acrylamide, ampholine, and Ficoll-Paque™ were purchased from GE Healthcare (Uppsala, Sweden); Agarose, Pro-Q® Diamond dye, SYPRO® Ruby and PeppermintStick™ Phosphoprotein Molecular Weight Standards were from Invitrogen™ (Carlsbad, CA, USA); piperazine di-acrylamide (PDA), TEMED, Bio Rad Protein Assay, IPG strips, were from Bio-Rad Laboratories (Hercules, CA, USA). Trypsin (sequencing grade modified) was from Promega (Madison, WI, USA). All solvents used were Ultra-Resi-Analyzed grade.
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3

Fabrication of Polyacrylamide Cell Substrates

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Polyacrylamide substrates were synthesized for cell analysis as previously described[17 ]. Two different rigidity substrates were fabricated: soft with 8% acrylamide (Sigma Aldrich) and 0.02% bis-acrylamide (~2 kPa, GE Healthcare Life Sciences) and hard (8% acrylamide and 0.06% bis-acrylamide, ~8 kPa). Briefly, glass coverslips were activated by incubation in 1% 3-aminopropyltriethoxysilane followed by 0.5% glutaraldehyde. acrylamide solutions were made with 200 nm red particles (Invitrogen) and ammonium persulfate and tetramethylethylenediamine were added to initiate gel polymerization. This solution was then added to glass slides and an activated coverslip added on top. In order to allow for cell adherence, the surface was activated with 0.2 mg/mL sulfosuccinimidyl-6-(4′-azido-2′-nitrophenylamino)-hexanoate (G-Biosciences) and coated with 0.2 mg/mL rat tail collagen I (Corning), which has previously been shown to play a critical role in MSC differentiation [18 (link)], overnight at 4°C with agitation. Substrates were sterilized under UV light and incubated in media for at least an hour before use. Mechanical properties of the substrates were assessed via compression testing using a Bose Endura TEC ELF 3200 Uniaxial Testing System (data not shown). The Young’s modulus was calculated from the slope of the linear region of the stress vs. strain curve at less than 10% strain.
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4

Acrylamide and Protein Molecular Weight Standards

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Acrylamide and molecular weight marker proteins were purchased from GE Healthcare (Uppsala, Sweden). Coomassie Brillant Blue G-250 was purchased from AppliChem GmbH (Darmstadt, Germany). All other chemicals were purchased from Sigma-Aldrich (St. Louis, MO, USA).
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5

Protein Separation and Identification

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Sephacryl S-200 HR and sodium hydrosulfite were obtained from Sigma-Aldrich chemicals Co., Sweden. The disposable PD-10 columns, IPG strips, DTT, Iodoacetamide, Acrylamide, Bis-Acrylamide, Glycine, Methanol, Glacial Acetic acid, β-mercaptoenthanol and Coomassie blue, were obtained from GE Health Care. HNE was obtained from Cayman Chemical Company. Dialysis tubing was sourced from Spectrum laboratories, Inc. (Rancho Domingues, CA, USA). OFFGEL starter kit was procured from Agilent Technologies. All chemicals were of reagent grade or greater purity.
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6

Recombinant Histone Purification Protocol

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Acrylamide, Bis-Acrylamide, SDS, tetramethylethylenediamine (TEMED), dithiothreitol and ammonium persulfate were purchased from GE Healthcare (Pittsburgh, PA, USA). BAC was purchased from Polysciences, Inc. (Warrington, PA, USA). Sequencing-grade trypsin was purchased from Promega (Madison, WI, USA). Recombinant human histone samples were purchased from New England Biolabs (Ipswich, MA, USA). Other chemicals unless specified were analytical grade and purchased from Wako (Osaka, Japan).
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7

Protein Extraction and Separation

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Acrylamide, bisAcrylamide, DTT, iodoacetamide, CHAPS, SDS, urea, glycerol, thiourea,
TEMED, ammonium persulfate (APS), molecular markers and IPG buffer were obtained from GE
Healthcare Life Sciences (São Paulo, SP, Brazil). Triton X-100, BSA and CBB were obtained
from SIGMA-ALDRICH (São Paulo, SP, Brazil). Trypsin was obtained from Promega (São
Paulo, SP, Brazil).
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8

Comprehensive Phosphoproteomic Sample Preparation

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Acetonitrile (ACN), acetone, trifluoroacetic acid (TFA), trichloroacetic acid (TCA), DL-dithiothreitol (DTT), iodoacetamide (IAA), glycine, EDTA, Tris, endonuclease, phosphoprotease and protease inhibitors, lanthanum chloride, potassium dihydrogen phosphate, Coomassie Blue G-250, imidazole, alkaline phosphatase were purchased from Sigma (Sigma Aldrich St.Louis, MO, USA); urea, CHAPS, SDS, glycerol, acrylamide, ampholine, and Ficoll-Paque™ were purchased from GE healthcare (Uppsala, Sweden); Agarose, Pro-Q® Diamond Phosphoprotein Enrichment kit, Pro-Q® Diamond dye, SYPRO® Ruby and PeppermintStick™ Phosphoprotein Molecular Weight Standards were from Invitrogen™ (Carlsbad, CA); piperazine di-acrylamide (PDA), TEMED, Bio Rad Protein Assay, IPG strips, were from Bio-Rad Laboratories (Hercules, CA). Trypsin (sequencing grade modified) was from Promega (Madison, Wisconsin, USA). All solvents used were Ultra-Resi-Analyzed grade.
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9

Antibody-based Protein Analysis Protocol

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EMEM (Eagle's minimum essential medium) was purchased from Sigma (St. Louis, MO). Foetal bovine serum (FBS) was obtained from Gibco. Antibodies; pan-Ras, c-Raf, RSK, phosopho-Elk1, c-Jun, phospho-JNK-1/2, c-myc, HIF-1α, Bcl-2, Bax, NFκB p50 and p52, VEGF, phospho-GSK3β, phospho-p38 MAPK and p53 were obtained from MERCK, San Diego, USA. While urea, CHAPS, DTT IPG buffer (pH 3-11NL), SDS, bromophenol blue Tris, glycine, acrylamide, bis-acrylamide were purchased from GE Healthcare.
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10

Proteomic Analysis of Bacterial Toxins

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Acrylamide (17-1302-02), bis-Acrylamide (17-1304-02), sodium dodecyl sulphate (SDS) (17-1313-01), HiTrap Protein-A Sepharose high-performance column (17-0402-01), and Superdex 75 Increase 10/300 GL (29148721) were acquired from GE Healthcare Life Sciences (São Paulo, SP, Brazil) . Azocasein (A2765), bromelain (code B4882), Lcysteine (C7352), O-phthaldialdehyde (P0657), β-mercaptoethanol (M6250), Evans blue dye (E2129), cholera toxin from Vibrio cholerae (C8052), Freund's complete (F5881) and incomplete (F5506) adjuvant, alkaline phosphatase-conjugated goat anti-rabbit IgG antibodies (A6066) and p-nitrophenylphosphate disodium (N2765) were obtained from Sigma-Aldrich (São Paulo, SP, Brazil). All other chemicals were of analytical grade.
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