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28 protocols using xf calibrant solution

1

Mitochondrial Dynamics and Energy Metabolism

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OCRs and ECARs were measured using an XF24 Extracellular Flux Analyser (Seahorse Bioscience, North Billerica, MA, USA). HeLa cells (15×103) transfected with siCtrl or siOPA1 were plated on XF24 microplates 3 days before OCR measurements. Dual-analyte sensor cartridges were soaked in XF Calibrant Solution (Seahorse Biosciences) in 24-well cell-culture microplates overnight at 37°C to hydrate. Approximately 1 h prior to experimentation, injection ports on the sensor cartridge were filled with oligomycin (1 µM), FCCP (1 µM), and rotenone (1 µM) plus antimycin A (1 µM). Plates were then loaded into the XF24 instrument for calibration. For measuring oxygen consumption, the DMEM of HeLa cells was replaced by DMEM supplemented with NaCl (143 mM), Phenol Red (3 mg/ml), glucose (10 mM), glutamine (2 mM) and pyruvate (2 mM) at pH 7.4, and the plates were maintained at 37°C 1 h prior to experimentation. Plates were then loaded into the Seahorse XF24 analyser following the manufacturer's instructions.
ATP measurements in HeLa cells were determined using an ATP Colorimetric/Fluorometric Assay kit (Abcam). Intracellular ATP levels were determined using the colorimetric assay, following the manufacturer's instructions, on 1.106 HeLa cells transfected with control siRNA or OPA1 siRNA. ATP content was measured in duplicate (570 nm) and calculated per microgram of protein.
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2

Seahorse XFe96 Assay for U2932 Cells

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Seahorse XFe96 sensor cartridge was hydrated in a utility plate with 200 μL of Seahorse XF Calibrant solution overnight at 37 °C with 0% CO2. One hour prior to assay, U2932 cells were plated at a density of 1×105 per 180 μL per well in a poly-D-lysine coated XF96 cell culture microplate with 6 replicates. Cells were plated in Seahorse XF RPMI medium containing 2.05 mM L-glutamine and 11.11 mM glucose. Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) was measured by the Seahorse XFe96 Analyzer.
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3

Measuring Neuronal Oxygen Consumption and ATP Levels

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Oxygen consumption rates (OCR) were performed using the XF24 Extracellular Flux Analyser (Seahorse Bioscience, North Billerica, MA). Neurons (3 × 105) transfected with siCtrl or siOPA1 were plated on XF24 microplates 6 days before OCR measurements. Dual‐analyte sensor cartridges were soaked in XF Calibrant Solution (Seahorse Biosciences) in 24‐wells cell culture microplates overnight at 37°C to hydrate the probes. One hour prior to experimentation, injection ports on the sensor cartridge were filled with oligomycin (0.6 μmol/L), carbonyl cyanide 4‐(trifluoromethoxy)phenylhydrazone (FCCP) (6 μmol/L), and rotenone (50 nmol/L) plus antimycin A (0.182 μmol/L). Plates were then loaded into the XF24 instrument for calibration. For oxygen consumption measurement, growth media of neurons were replaced with incubation media (DMEM supplemented with NaCl (143 mmol/L), phenol red (3 mg/mL), glucose (10 mmol/L), glutamine (2 mmol/L), and pyruvate (2 mmol/L) at pH 7.4, and kept at 37°C, 1 h prior experimentation. The XF24 microplate was then loaded into the Seahorse XF24 analyzer following the manufacturer's instructions.
ATP and ADP measurements in siOPA1‐ or siCtrl‐transfected neurons were determined using a bioluminescence technique using an ATP monitoring kit as described previously.24
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4

Metabolic Assays for Cell Viability

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Rotenone, carbonyl cyanide ptrifluoromethoxyphenyl- hydrazone (FCCP), oligomycin, and 2-deoxy-D-glucose (2-DG) were from Sigma (St Louis, MO). Dulbecco's modified Eagle's medium (DMEM) was from Gibco (USA). Fetal bovine serum (FBS) was from NATOCOR (Argentina). Cell Counting Kit-8 (CCK-8), BCA protein assay kit, ATP assay kit, ROS assay kit and crystal violet dye were obtained from Beyotime Institute of Biotechnology (Nanjing, China). XF assay medium and XF calibrant solution were obtained from Seahorse Bioscience (USA). RNA Extraction Kit, PrimeScript RT reagent kit, and SYBR Premix Ex Taq were from TakaRa Biotechnology (Dalian) Co, Ltd (Dalian, China).
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5

Measuring ALKBH7 Knockdown Effects on Mitochondrial Energy

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ALKBH7-knockdown effects on mitochondrial energy activity41 (link) were measured using a Seahorse Bioscience XF96 analyser (Seahorse Bioscience Inc.) and the Seahorse XFp Cell Energy Phenotype Test Kit (Agilent) according to the manufacturer’s instructions. Both siControl and siALKBH7 HepG2 cells were seeded at 2 × 104 cells per well with 7 replicates in Seahorse XF96 cell culture microplates (Agilent). Cells were grown overnight and incubated with XFp medium for around 1 h in a non-CO2 incubator before initiating the cell energy phenotype assay. The 96-well sensor cartridge was hydrated in 200 μl XF calibrant solution (Seahorse Bioscience Inc.) overnight at 37 °C before plate calibration. For the cell energy phenotype assay, cells were treated with 1 μM oligomycin followed by three serial injections of FCCP at final concentrations of 0.5, 1.0 and 2.0 μM. Seahorse Wave software (v2.6) was used for data processing, including detection of outliers and cell number normalization. The final reports for the oxygen consumption rate and extracellular acidification rate signals were generated using the Seahorse XF Cell Energy Phenotype report generator.
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6

Quantifying Cellular ATP Production Dynamics

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For the seeding of cells, cell counting was performed and around 2650 cells were seeded in each well of a Agilent Seahorse XF96 Cell Culture Microplates. The plate was incubated for 72 h before the siRNA treatment was done. Measurement of ATP production rate in cells was performed using the Seahorse XF Real-Time ATP Rate Assay Kit according to the manufacturer's instructions. Briefly, Seahorse XF96 fluxpak cartridges were hydrated using Seahorse XF Calibrant Solution, 24 h pre-measurement. On the day of measurement, the culture medium was replaced with Seahorse XF DMEM medium (2 mM glutamine, 1 mM pyruvate, 10 mM glucose) and cells were incubated for 1 h at 37°C without additional CO2. Measurement was performed using the standard program for the ATP rate assay kit (Oligomycin injection after 18min, Rotenone/Antimycin A injection after 36 min). Acquired data were normalized to cell numbers via Hoechst33342 staining. Measurement of fluorescence intensity was performed using a Tecan Infinite® M1000 PRO.
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7

Measuring Mitochondrial Respiration in NPCs

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We used a Seahorse XF24 Extracellular Flux Analyzer (Seahorse Biosciences; North Billerica, MA, USA) to measure the oxygen consumption rate (OCR) in the cells. We seeded the dissociated NPCs onto 24-well Seahorse microplates at a density of 1.5×105 cells per well. Before taking the measurements, we soaked the sensor cartridges in XF Calibrant Solution (Seahorse Biosciences) in 24-well cell culture microplates overnight at 37℃ to hydrate them. We filled the injection ports on the sensor cartridge with drugs from an XF Cell Mito Stress Test Kit (Seahorse Bioscience): oligomycin (1 µM), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) (1 µM), and rotenone (1 µM) with antimycin A (1 µM). The XF24 microplate was loaded into the Seahorse XF24 analyzer according to the manufacturer's instructions. All experiments were carried out at 37℃.
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8

Mitochondrial Dysfunction and Cell Viability

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L-Carnosine, sodium pyruvate, rotenone, carbonyl cyanide p-trifluoromethoxyphenyl-hydrazone (FCCP), antimycin A, 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetra-zolium bromide (MTT), methanol, lactic acid were from Sigma (St. Louis, MO, USA). Penicillin, streptomycin, L-glutamine, trypsin, Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum were from GIBCO-BRL (Grand Island, NY, USA). Annexin V-FITC/PI apoptosis detection kit, BCA Protein Assay Kit and ATP Assay Kit were bought from Beyotime Institute of Biotechnology ((Nanjing, China). XF assay medium and XF calibrant solution were bought from Seahorse Bioscience.
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9

Anther Respiration Measurement with Seahorse

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Anther respiration was measured using a Seahorse XF analyzer (Seahorse Bioscience, Billerica, MA, USA) following a published method (Sew et al., 2013 (link)) and the manufacturer’s instructions. Briefly, the eight‐well sensor cartridge was hydrated in 200 μl of XF Calibrant Solution (Seahorse Bioscience) per well for 2 h at room temperature before the assay. Anthers at the YM, VP, and BN stages were fixed at the bottom of wells with 1 μl tissue adhesive glue (3 M Vetbond Tissue Adhesive, Neuss, Germany). After 2 min, 180 μl of respiration buffer (2 mm HEPES, 2 mm MES, and 0.4 mm CaCl2, pH 7.6) was added to the wells, followed by eight cycles of mixing (2 min), waiting (3 min), and measurement (5 min). The OCRs of anthers were recorded by Seahorse XF Acquisition and Analysis Software (v.2.6; Seahorse Bioscience).
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10

Extracellular Acidification Measurement in Cells

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Measurement of extracellular acidification rate (ECAR) was performed in a 96-well XF Extracellular Flux Analyser (Seahorse Biosciences). Sensor cartridge injection compounds or XF Base Media controls were injected in a total volume of 25 μl. Injection compound concentrations were as follows: glucose (5 mM), oligomycin (OLIGO) (mitochondrial ATP synthase inhibitor) (2.5 μM), 2-DG (100 mM). Sensor cartridges (96-well) were hydrated for a minimum period of 12 h with XF Calibrant solution according to the manufacturer’s instructions (Seahorse Biosciences, North Billerica, MA, USA). XF Assay Base Media (Seahorse Biosciences) was supplemented with l-glutamine (2 mM) for ECAR measurement. Glycolysis parameters [glycolysis, glycolytic capacity (GC), glycolytic reserve (GR)] were calculated as follows: Glycolysis: (Maximal rate measurement after glucose injection through measurement prior to oligomycin (OLIGO) injection) minus (measurement prior to glucose injection); GC: (Maximal rate measurement after OLIGO injection through measurement prior to 2-DG injection) minus (measurement prior to glucose injection); GR: GC minus glycolysis (23 (link)).
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