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Xf dmem base medium

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The XF DMEM base medium is a cell culture medium formulated for use with Agilent's Seahorse XF Analyzers. It is a basal medium that provides the necessary nutrients and buffering capacity to support the growth and metabolism of cells under extracellular flux analysis conditions.

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11 protocols using xf dmem base medium

1

Measuring Cellular Oxygen Consumption

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Oxygen consumption rates (OCRs) were measured as previously described [24 ] with minor modification using Seahorse Bioscience XFp Analyzer (Agilent, USA). For the measurement of OCRs, cells were incubated in XF DMEM base medium (pH 7.4; Agilent, USA) containing 25 mM D-glucose (Sigma, USA) and 4 mM L-glutamine (Sigma, USA) at 37 °C. XFp Cell Mito Stress Test Kit (Agilent, USA) was used (2.5 μM of oligomycin, 0.5 μM of FCCP and 0.5 μM of rotenone/antimycin A) [21 (link)]. Basal and maximal respiration was calculated by subtraction of non-mitochondrial respiration. Proton leak related OCR was calculated by subtracting rotenone/antimycin A induced OCR from the oligomycin A-induced OCR [24 ]. OCRs were normalized with protein concentrations. The data were analyzed by Agilent Wave software (version 2.6.0.31).
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2

Extracellular Flux Assay of BMDC Metabolism

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The Seahorse XFp Extracellular Flux Analyzer (Agilent, Santa Clara, CA) was used to analyze real-time changes of extracellular acidification rates (ECARs) as described earlier (48 (link)). BMDCs were plated (120,000 cells/well) in 200 µL in XFp mini-culture plates overnight in an IMDM medium containing 5% FBS at 37°C in the CO2 incubator. The culture medium was replaced the next day with a fresh medium containing 5% FCS, stimulated with HDM (100 µg/mL), and treated with and without rSPLUNC1 protein for 16 h. Furthermore, the medium was replaced with a warm XF DMEM base medium (Agilent) containing 2 mM L-glutamine (Agilent, 103579) and 1% FBS. The assay plate was incubated in a non-CO2 incubator for 1 h at 37°C. Glycolysis stress tests were performed according to the manufacturer’s protocol with sequential injections of glucose, oligomycin (Agilent), and 2-DG (Sigma) in ports A, B, and C, respectively. The effects on ECAR were recorded three times every 5 min interval, and data were analyzed using Wave software 2.6.1 (Seahorse Bioscience) after normalization with total protein.
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3

Extracellular Flux Analysis of Macrophage Metabolism

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After culture for 7 days, macrophages were seeded into XFe96 microplates at a density of 1 × 105 cells per well and cultured overnight. Cells were treated with or without 100 ng/ml LPS for 6 h before extracellular flux analysis was performed. The culture medium was switched to XF DMEM base medium (Cat No. 103575-100, Agilent) supplemented with glucose (10 mM), pyruvate (1 mM), and glutamine (2 mM). Cells were incubated in a non-CO2 incubator at 37 °C for 1 h. The extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) were measured using an XFe96 analyzer after sequential injection of the compounds of the XF Glycolysis Stress Test Kit (Cat No. 103020-100, Agilent) (rotenone and antimycin A (0.5 μM) and 2-deoxyglucose (50 mM)) or the XF Cell Mito Stress Test Kit (Cat No. 103015-100, Agilent) (oligomycin (1.5 µM), FCCP (2 µM), and rotenone and antimycin A (0.5 µM)). The ECAR and OCR were automatically calculated by Seahorse XFe96 software (Seahorse Bioscience, Agilent).
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4

Adipocyte Respiration Profiling by Seahorse XF

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Oxygen consumption rates (OCRs) were measured by the Seahorse XF Analyzers (Agilent)32 (link),33 . Primary cultured adipocytes from gWAT of WT or TMEM86A AKO, differentiated C3H10T1/2 adipocytes overexpressing Mock or TMEM86A, and differentiated C3H10T1/2 adipocytes treated with either vehicle, LPC P-18:0 (10 μM), or LPE P-18:0 (10 μM) were washed and maintained in assay medium (XF DMEM Base Medium, pH 7.4 (Agilent, cat#103575-100)) supplemented with D-(+)-glucose (25 mM) and L-glutamine (4 mM) at 37 °C. XFp Cell Mito Stress Test Kit (Agilent, cat#103010-100) was used with the following concentrations: 2.5 μM of oligomycin, 0.5 μM of carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP), and 0.5 μM Rotenone/Antimycin A. Basal and maximal OCRs were calculated by subtraction of non-mitochondrial respiration. ATP production-related OCRs were calculated by subtracting the oligomycin A-induced OCR from the basal OCR. Spare respiratory capacity was calculated by subtracting Basal OCR from Maximal OCR. Proton leak was calculated by subtracting non-mitochondrial respiration from the oligomycin A-induced OCR. OCRs were normalized with protein concentrations. Agilent Wave software (version 2.6.0.31) was used to analyze the data.
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5

Cellular Oxygen Consumption Measurement

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XFp Analyzers were used to measure oxygen consumption rate (OCR). Cells were incubated in XF DMEM base medium (Agilent, 103575-100, pH 7.4, Cedar Creek, Texas, USA) supplemented with 4 mM L-glutamine (Sigma, G8540, St. Louis, MO, USA) and 25 mM D-glucose (Sigma, G7021, St. Louis, MO, USA) at 37 °C for the measurement. XFp Cell Mito Stress Test Kit (Agilent, 103010-100, Cedar Creek, Texas, USA) was sequentially prepared with the following optimal final concentrations: 2.5 μM oligomycin, 0.5 μM FCCP, and 0.5 μM rotenone/antimycin A, and basal, maximal, proton leak and were calculated previously described [14 (link)].
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6

Evaluating STAT3 Inhibitors in Cancer Cells

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STAT3 inhibitors - Stattic, cryptotanshinone, WP1066 and STA21 were obtained from Selleck Chemicals (Houston, TX, USA). TTI-101 was custom synthesized by Regis technologies Inc. (Morton Grove, IL, USA). Molecular grade dimethyl sulfoxide (DMSO), reduced glutathione (GSH), iodoacetamide, and N-ethylmaleimide were obtained from Sigma-Aldrich (St. Louis, MO, USA). Cisplatin was acquired from (TEVA Pharmaceuticals, North Wales, PA). All LC/MS reagents, including ammonium acetate, formic acid, acetonitrile, methanol and water, were obtained from Honeywell Fluka (Morris Plains, NJ, USA). STAT3 antibody was purchased from Cell Signaling Technology (Danvers, MA, USA). Antibodies to histone H2B (ab52484) and GAPDH (ab9485) were purchased from Abcam (Toronto, ON, Canada). Antibody to Vimentin (sc66002) was obtained from Santa Cruz Biotechnology (Dallas, TX, USA). DMEM XF base medium, FCCP, and rotenone/antimycin A were obtained from Agilent Technologies (Santa Clara, CA, USA). A C18 Synergi™ 4 μm Fusion-RP 80 Å LC column (50 × 2 mm) was purchased from Phenomenex, (Torrance, CA, USA); a Waters Symmetry C18 column (100 Å, 3.5 μm, 4.6 mm × 150 mm) was purchased from Waters (Milford, MA, USA).
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7

Evaluating STAT3 Inhibitors in Cancer Cells

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STAT3 inhibitors - Stattic, cryptotanshinone, WP1066 and STA21 were obtained from Selleck Chemicals (Houston, TX, USA). TTI-101 was custom synthesized by Regis technologies Inc. (Morton Grove, IL, USA). Molecular grade dimethyl sulfoxide (DMSO), reduced glutathione (GSH), iodoacetamide, and N-ethylmaleimide were obtained from Sigma-Aldrich (St. Louis, MO, USA). Cisplatin was acquired from (TEVA Pharmaceuticals, North Wales, PA). All LC/MS reagents, including ammonium acetate, formic acid, acetonitrile, methanol and water, were obtained from Honeywell Fluka (Morris Plains, NJ, USA). STAT3 antibody was purchased from Cell Signaling Technology (Danvers, MA, USA). Antibodies to histone H2B (ab52484) and GAPDH (ab9485) were purchased from Abcam (Toronto, ON, Canada). Antibody to Vimentin (sc66002) was obtained from Santa Cruz Biotechnology (Dallas, TX, USA). DMEM XF base medium, FCCP, and rotenone/antimycin A were obtained from Agilent Technologies (Santa Clara, CA, USA). A C18 Synergi™ 4 μm Fusion-RP 80 Å LC column (50 × 2 mm) was purchased from Phenomenex, (Torrance, CA, USA); a Waters Symmetry C18 column (100 Å, 3.5 μm, 4.6 mm × 150 mm) was purchased from Waters (Milford, MA, USA).
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8

Extracellular Acidification of Mouse Urothelial Cells

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After the urothelial cells were scrapped off from freshly dissected mouse bladders, they were digested in a Liberase solution (Roche Diagnostics, Florham Park, NJ) at 37°C for 20 min. The reaction was stopped by the addition 2% fetal bovine serum containing 0.2 M EDTA. The urothelial cell suspension was then transferred into 24-well plates pre-coated with poly-L-lysine (Seahorse Bioscience, Santa Clara, CA) and incubated with XF Base DMEM medium (Agilent, Santa Clara, CA) at 37 °C in 5% CO2. For determination of extracellular acidification rate (ECAR), the following were added: 10 mM glucose, 0.5 μM Rot/AA (rotenone/antimycin A) and 50 mM 2-DG (2-deoxy-glucose) (Agilent, Santa Clara, CA, USA) at the time points indicated in Fig. 8 into XFe24 extracellular flux analyzer (Agilent, Santa Clara, CA).
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9

Urothelial Cell Metabolic Profiling

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Urothelial cells were harvested from the mucosal surfaces of the inside-out mouse bladders. The cells were incubated in a Liberase solution at 37 °C for 15 min, after which the digestion was stopped by adding 2% fetal bovine serum and 0.2 μM EDTA. The cells were then cultured in cell culture microplates pre-coated with poly-l-lysine (Seahorse Bioscience, Santa Clara, CA, USA) at 3 × 104 cells/well density in 500 µl XF Base DMEM medium (Agilent, Santa Clara, CA, USA) and incubated at 37 °C in 5% CO2. The assays were conducted at different time points by adding glucose, Rot/AA, and 2-DG successively in an XFe24 extracellular flux analyzer (Agilent, Santa Clara, CA, USA), and the ECAR data were recorded automatically.
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10

Mitochondrial Function Analysis in iPSC-Derived RPE Cells

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Analysis of mitochondrial function was performed on live cells using the XFe96 Extracellular Flux Analyzer (Agilent Technologies, Santa Clara, California, http://www.agilent.com) and the Seahorse XF Cell Mito Stress Test (CMST) Kit (Agilent Technologies). To avoid differences due to unequal growth rates, iPSC‐derived RPE cells were seeded onto a laminin‐coated 96‐well plate with a seeding density of 4 × 104 cell/well and grown until confluent. Data were normalized by cell count. Cells were stained with DAPI and counted by ImageJ software (National Institute of Health, Bethesda, Maryland, http://www.nih.gov). Cells were then washed with CMST assay medium (XF base medium DMEM supplemented with 2 mM glutamine, 5.5 mM glucose, and 1 mM sodium pyruvate, pH 7.4; Agilent Technologies), followed by incubation for 1 hour at 37°C in a non‐CO2 incubator. Oxygen consumption rate was detected under basal conditions followed by the sequential addition of oligomycin, carbonyl cyanide 4‐(trifluoromethoxy) phenylhydrazone (FCCP), rotenone, and antimycin A. From these sequential additions, the following parameters can be derived: basal respiration, ATP production, maximal respiration, and spare respiratory capacity.
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