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8 protocols using ethylene glycol tetraacetic acid (egta)

1

Spinal Cord Protein Extraction Protocol

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In this study, we modified the extraction method of Sahara et al.[19 (link)]. Spinal cord tissues were homogenized in 19 volumes (w/v) of extraction buffer containing 50 mM Tris-HCl (pH7.5), 5 mM EDTA (Nippon Gene, Tokyo, Japan), 1 mM EGTA (Nacalai tesque), 1% NP-40 (Sigma Aldrich), 0.25% deoxycholic acid sodium salt (Sigma Aldrich), 0.1 M NaCl, 0.5 mM PMSF (Sigma Aldrich), 1 × PhosSTOP (Roche, Basel, Schweiz), and 1 × Complete EDTA(-) (Roche). Homogenates were centrifuged at 250,000g at 4°C for 20 minutes. The supernatants were collected as the tris buffer-soluble fraction (S1), and 10 volumes (tissue weight/volume) of sarkosyl buffer containing 10 mM Tris-HCl (pH7.5), 0.5M NaCl, 1 mM EGTA, 10% sucrose (Wako Pure Chemical), and 1% sarkosyl were added to precipitates followed by sonication. The solutions were incubated at 37°C for 60 minutes, and centrifuged at 250,000g at 4°C for 20 minutes. The supernatants were collected as the sarkosyl-soluble fraction (S2), and 10 volumes (tissue weight/volume) of PBS (Nacalai tesque) were added to precipitates followed by sonication (sarkosyl-insoluble fraction, P2).
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2

Inhibitor Reagents for Cellular Experiments

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NMDA and calpain inhibitor-I were obtained from Sigma-Aldrich (St. Louis, MO, USA), EGTA was obtained from Wako Chemicals (Osaka, Japan), Jasplakinolide and Latrunculin A were obtained from Enzo Life Sciences (Farmingdale, NY, USA), and rose bengal was obtained from Nacalai Tesque (Kyoto, Japan).
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3

Microvessel Protein Extraction and Quantification

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The microvessels were homogenized in phosphoprotein lysis buffer containing 10 mM Tris-HCl (pH 6.8; Nacalai Tesque; 35434–34), 100 mM NaCl (Sigma; 28-2270-5), 1 mM EDTA (pH 8.0; Wako; 311–90075), 1 mM EGTA (Wako; 346–01312), 10% glycerol, 1% Triton-X100 (Sigma; X100), 0.1% sodium dodecyl sulfate (SDS; Nacalai Tesque; 02873–75), 0.5% sodium deoxycholate (Sigma; D6750), 20 mM sodium pyrophosphate (Sigma; S6422), 2 mM sodium orthovanadate (Sigma; S6508), 1 mM sodium fluoride (Wako; 196–01975), 1% protease inhibitor cocktail (Sigma; P2714), 1% phosphatase inhibitor cocktail 2 (Sigma; P5726), 1% Phosphatase Inhibitor Cocktail 3 (Sigma; P0044), and 1 mM PMSF (Sigma) using an electric mixer, and then sonicated on ice. Samples were centrifuged at 15,000 × g for 15 min at 4°C, and the supernatants were collected. The total protein concentration in the lysates obtained from microvessels was determined using a Pierce BCA Protein Assay Kit (Thermo Fisher Scientific; 23225).
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4

Isolation of Liver Cell Fractions

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At weeks 0, 1, 2, 3, 4, and 6 after 2-AAF/PH treatment, the rats were subjected to a standard two-step collagenase perfusion for isolation of liver parenchymal and non-parenchymal fractions following a published protocol [29 (link)]. Briefly, the rat was anesthetized and cannulated via the portal vein, and the liver was perfused with buffer containing 0.5 mM thylene glycol tetraacetic acid (EGTA; Wako), followed by perfusion solution containing 0.5 mg/ml collagenase (Worthington Biochemical, Lakewood, NJ, United States). Following perfusion for 20 min, the cells were detached by gentle shaking of the liver and dispersed into Williams’ Medium E (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS; Gibco). The suspended cells were collected and filtered through gauze and then washed three times, followed by centrifugation at 50×g for 2 min. The cell pellets were collected as parenchymal cells (PCs), and the supernatants were obtained as non-parenchymal cells (NPCs).
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5

Molecular Regulation of Myoblast Differentiation

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C2C12 myoblasts described previously (4 (link)) or mouse primary myoblasts were maintained and induced to differentiate into myotubes, and they were treated with STO-609 (Calbiochem), EGTA (Wako), GsMTx-4 (Peptide Institute), Yoda1, nifedipine (Wako), or tranilast (Tokyo Chemical Industry). Adenoviral vectors for LacZ and mouse KLF15 were described previously (35 (link)). Mouse KLF15 and negative control siRNAs were obtained from Invitrogen and were delivered into cells with the use of the Lipofectamine RNAiMAX transfection reagent (Invitrogen). Isolation of total RNA and quantitative RT-PCR analysis were performed as previously described (4 (link)). Data were normalized by the amount of 36B4 mRNA. The sequences of PCR primers are provided in Supplemental Tables 2 and 3. Immunoblot analysis was performed with antibodies against STAT3 (4904, Cell Signaling Technology) and against Tyr705-phosphorylated STAT3 (9131, Cell Signaling Technology). Uncropped immunoblots are presented in Supplemental Figure 12.
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6

Notch Ligand Recombinant Proteins

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Human IgG1 Fc-fused recombinant human DLL1 (DLL1-Fc), DLL4 (DLL4-Fc), and JAG1 (JAG1-Fc), and Flag-tagged human JAG2 (JAG2-Flag) were as described [27] (link), [28] (link). Human IgG1 (Sigma, St Louis, MO) was used as a control for recombinant Notch ligands. EGTA, sodium azide (NaN3), and DMSO were purchased from Wako Pure Chemical Industries (Osaka, Japan). A γ-secretase inhibitor, N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT) was purchased from the Peptide Institute (Osaka, Japan).
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7

Primary Hepatocyte Isolation via Collagenase Perfusion

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Primary hepatocyte isolation was performed using two-step collagenase perfusion technique, as previously described [27] . Briefly, a C57BL6/J mouse was anesthetized with isoflurane (Wako) and the inferior vena cava was exposed and cannulated with a 25-gauge needle. After clamping the superior vena cava and cutting the hepatic portal vein, the liver was perfused with 50 mL of Ca 2+ -free HBSS containing 0.5 mM EGTA (Wako) and 2 U/mL heparin (Novo-Heparin; Mochida, Tokyo, Japan) for 7 min, followed by 100 mL of collagenase solution containing 0.2% dispase II (Sanko Junyaku, Tokyo, Japan), 0.2% collagenase type II (Gibco, Palo Alto, CA, USA), 0.1 mg/mL DNase I (from bovine pancreas, Sigma), heparin 2 U/mL, 150 mmol/L NaCl, 5.4 mmol/L KCl, 0.34 mmol/L NaHPO 4 , 0.1 mmol/L MgSO 4 , 5.0 mmol/L CaCl 2 , 4.2 mmol/L, NaHCO 3 , 5.6 mmol/L glucose, and 10 mmol/L HEPES (all of the chemical reagents other than those indicated were purchased from Wako) for 7 min at 37°C. The liver was then resected out and gently shaken to retrieve the cells.
After filtering the isolated cells through a 100 µm strainer (BD Falcon, Franklin Lakes, NJ, USA), the cell suspension was washed three times by centrifugation at 50 × g for 3 min at 4°C. The isolated primary hepatocytes were immediately used for RNA extraction or the recellularization procedure.
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8

Regulation of Calcium Signaling

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D-glucose, diazoxide (DZ), diltiazem, and EGTA were purchased from Wako Pure Chemicals (Osaka, Japan). Fluo3 acetoxymethylester (Fluo3-AM), NNC55-0396, tolbutamide (TB), and u-conotoxin (u-CgTX) GVIA were purchased from Sigma-Aldrich.
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