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9 protocols using bapta am

1

Assessing Ramos and BCL Cell Expansion

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Ramos cells and #1542B BCL cells were treated with the cell-permeable Ca2+ chelator BAPTA AM [(10 µM) 1,2-Bis(2-aminophenoxy) ethane; Santa Cruz Biotechnology]; or CsA (0.5 µg/ml) for 4 h. To assess the expansion of Ramos and #1542B BCL cells, BAPTA AM was added in concentrations of 5, 10, 20 and 40 µM, and DMSO was used as a control. Half of the medium (including inhibitors) was renewed daily.
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2

Lysosomal Function and Regulation Assays

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Carbonyl cyanide 3-chlorophenylhydrazone (CCCP), ethylene glycol tetra acetic acid (EGTA), hydrogen peroxide solution (H2O2), d-mannitol, and lipopolysaccharides were purchased from Sigma-Aldrich, USA. Bafilomycin A1 and GPN were from Santa Cruz Biotechnology, while BAPTA-AM, cyclosporin A, FK506, ionomycin, nicotinic acid adenine dinucleotide phosphate (NAADP), trans-Ned-19 (Ned-19), and U18666A were from Tocris Biosciences, USA. Thapsigargin (TG) was bought from Almone Labs, USA, while LysoTracker Red DND-99 Dye and Rhod dextran were from Invitrogen, USA. Antibodies used for immunoblotting and immunostaining were as follows: anti-mouse lysosome-associated membrane protein-1 (LAMP-1; sc-20011, Santa Cruz Biotechnology, USA), anti-rabbit cathepsin D (2284S, Cell Signaling, USA), anti-rabbit caspase-1 (2225S, Cell Signaling, USA), anti-rabbit TFEB (37785S, Cell Signaling, USA), anti-rabbit histone H3 (D1H2) (4499S, Cell Signaling, USA), anti-rabbit Integrin β1 (4706S, Cell Signaling, USA), anti-rabbit GAPDH (2118S, Cell Signaling, USA), and anti-rabbit α/β-tubulin (2148S, Cell Signaling, USA).
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3

Comprehensive Reagent Inventory for Cell Signaling Research

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All chemicals and reagents were purchased from Sigma, unless otherwise stated. The following reagents from other suppliers were used: thapsigargin (Calbiochem, 586005, USA), compound C (Calbiochem, 171260, USA), BAPTA/AM (Santa Cruz, USA), bafilomycin A1 (Calbiochem, 196000, USA), STO‐609 (Calbiochem, 570250, USA), celastrol (cdmust, A0106, China), methotrexate (MTX; LC labs, MA, USA), RIPA (CST, 9806, USA), Fluo‐3, AM (Life Technologies, F14218, USA), EnVision™ FLEX Target Retrieval Solution, High pH (50×; DAKO, DM828, USA), antibodies light‐chain 3B (LC3B) rabbit mAb (Cell signaling, 2775/3868, USA, RRID:AB_915950), phospho‐p70S6 kinase (Thr389) rabbit mAb (CST, 9205, USA), p70S6 kinase rabbit mAb (CST, 9202, USA), phospho‐AMP‐activated protein kinase (AMPK; Thr172) rabbit mAb (CST, 2531, USA), AMPK rabbit mAb (CST, 2532, USA), vimentin mouse mAb (Abcam, 8978, USA), anti‐β‐of actin mouse monoclonal IgG1 (Santa Cruz, sc‐47778, USA), rabbit anti‐mouse IgG (H + L) secondary antibody TRITC (Invitrogen, PA1‐28565, USA), and GOXMO TRITC HIGH XADS (Invitrogen, A16083, USA).
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4

Focal Adhesion Kinase Regulation

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Polyclonal rabbit anti-focal adhesion kinase (FAK) and polyclonal rabbit anti-phospho-Tyr397-FAK were purchased from Cell Signaling (Danvers, MA, United States), polyclonal rabbit anti-MMP1 from Abcam (Cambridge, United Kingdom) and monoclonal anti-β-actin from Sigma (Munich, Germany). Polyclonal rabbit anti-mouse, anti-goat and anti-rabbit IgGs were acquired from Dako (Glostrup, Denmark). Apigenin and luteolin were purchased from Sigma (Munich, Germany) and human recombinant MMP1 from Sigma-Aldrich (SRP3117, St. Louis, MO, United States). U73122 was obtained from Calbiochem (Darmstadt, Germany), BAPTA-AM was from Santa Cruz Biotechnology (Heidelberg, Germany).
siRNAs targeting human MLC2 (MYL2; SMART pool, ON-TARGET PLUS, Cat. No.: L-011087000005, siRNAs targeting human FAK (SMART pool, ON-TARGET PLUS, Cat. No.: L-003164000005) were ordered from Dharmacon (Gene Expression and Gene Editing, GE Healthcare, Lafayette, CO, United States). Non-targeting (n.t.) control siRNA (Silencer® Select Negative Control No. 1 siRNA, Cat. No.: 4390843) was purchased from Ambion (Life Technologies, Carlsbad, CA, United States). All siRNAs were re-suspended in RNAse-free water to yield a stock concentration of 20 μM.
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5

Pulmonary Artery Smooth Muscle Cell Hypoxia Response

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PASMCs were identified by expression of α-actin (≥ 95% of the cells) by immunofluorescence using an antibody against α-SMA (1:200, Abcam, USA). Primary human pulmonary artery SMCs (ScienCell Research Laboratories, USA) were maintained in a Petri dish containing prechilled PBS, 2% penicillin–streptomycin, Ca2+-free HBSS, and 0.5% fetal calf serum mixed with 20% DMEM/F12 medium (Billups-Rothenberg, Del Mar, USA). Then, the cells were cultured in an atmosphere containing 5% CO2 and 21% O2 or 3% O2 in a humidified incubator at 37 °C for 3, 6, 12, 24, and 48 h for normoxia or hypoxia treatments, respectively. For cell proliferation, Ca2+ imaging, and detection of the phosphorylation signaling pathway, PASMCs were pretreated with cyclopiazonic acid (CPA), nifedipine (Nifed), EGTA (Santa Cruz, USA), BAPTA/AM (Santa Cruz, USA), LY294002 (Santa Cruz, USA), Perifosine (Santa Cruz, USA), LY317615 (Santa Cruz, USA), rapamycin (Santa Cruz, USA), or PD98059 (Santa Cruz, USA) and seeded onto 25 mm glass coverslips as indicated. Then, various concentrations of recombinant human RELM-β protein (0–40 ng/ml, Abgent, USA) were used to stimulate PASMCs for various periods (0–72 h). Cells of passages 3–7 were used in the experiments. When cells in the logarithmic growth phase reached a density of 70%, cell cycle was synchronized by incubation in the serum-free medium for 24 h.
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6

Osteosarcoma and Chondrosarcoma Cell Culture

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MG63 (osteosarcoma) and sw-1353 (chondrosarcoma) cell lines were purchased from the American Type Culture Collection (Teddington, UK) and cultured in DMEM (Sigma- Aldrich, St Louis, MO, USA) medium supplemented with 10% v/v Fetal Bovine Serum (FBS; Gibco, Invitrogen Life Technologies, Barcelona, Spain), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Spain) in a humidified atmosphere of 5% CO2 at 37 °C. Cells were sub-cultured once a week using a 0.25% trypsin solution. Compound concentrations used for the experiments were: 1 mM melatonin, 5 µM BAPTA, 3 mM calcium chloride, 100 µM trolox and 100 µM ascorbate (Sigma-Aldrich, St Louis, MO, USA). Culture flasks and dishes were obtained from Fisher Scientific (Madrid, Spain). Fluo-3AM and Rhod-2 were purchased from Invitrogen (Invitrogen Life Technologies, Barcelona, Spain) and BAPTA/AM was acquired from Santa Cruz (Santa Cruz Biotechnology, Dallas, TX, USA). All other reagents were purchased from Sigma (Sigma-Aldrich, St Louis, MO, USA), unless otherwise indicated.
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7

Celastrol Effects on RASF Transcriptome

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RNA was extracted using RNeasy Mini Kit (Qiagen, USA) from RASFs untreated (control), treated with celastrol [1 μM], or celastrol in the presence of BAPTA/AM [10 μM] (Santa Cruz, USA) for 24 h. RNA concentration was determined using the NanoDrop 2000c Spectrophotometer (Thermo Scientific) and 1 μg of RNA was used to synthesize cDNA with RT2 First Strand Kit (Qiagen, USA). Three independent biological samples were employed.
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8

EGF, DCA, and Ionomycin Treatment of HT-29 Cells

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HT-29 cells were plated in 6 well dishes at a density of 1.0×106 cells/well and cultured in 10% complete media for 24 hours to allow for adherence. After 24 hours, the complete media was replaced with serum-free media for 18 hours prior to any treatment. Cells were then treated with human recombinant EGF (Corning Inc.), DCA (Sigma-Aldrich, St. Louis, MO), or ionomycin (Sigma-Aldrich). In some studies pretreatment of HT-29 cells with inhibitors including PD153035 1μM (Santa Cruz Biotechnology, Dallas, Texas), BAPTA-AM (Santa Cruz Biotechnology), SKI (Santa Cruz Biotechnology) or Kn-93 (Cayman Chemical, Ann Arbor, MI) preceded treatments. Treated cells were washed with PBS, scraped and lysed with RIPA buffer containing HALT protease and phosphatase inhibitor cocktail (ThermoFisher Scientific, Waltham, MA) at various time points. Lysates were sonicated and spun down, removing contaminating DNA and cell debris. Protein was harvested from the supernatant and quantified using a BCA protein assay kit (ThermoFisher Scientific).
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9

Polydatin Modulates Calcium Levels in Colon Cancer

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The colon cancer cell lines were transferred onto six-well plates and maintained with different doses of polydatin (0, 100, 200, and 300 μM), or polydatin (300 μM) with calcium chelators, including 2-aminoethoxydiphenyl borate (2-APB; Cat No: D9754, Sigma-Aldrich), and 1,2-bis (2-aminophenoxy) ethane-N,N,N′,N′-tetra-acetic acid tetrakis (BAPTA/AM; Cat No: sc-202488, Santa Cruz Biotechnology), for 24 h. These cells were stained by Rhod-2 dye for 30 min. Fluorescence levels were estimated using a flow cytometer. The experiment was conducted in triplicate.
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