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9 protocols using xf real time atp rate assay kit

1

Quantifying Hepatocyte Respiration and ATP Dynamics

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The respiration activity in primary hepatocytes was measured at 37 °C by high-resolution respirometry with the Seahorse Bioscience XF24-3 Extracellular Flux Analyzer. Succinate (10 mM) and rotenone (2 μM) were used as substrates to quantify State 2. State 3 was initiated with ADP, State 4 induced with the addition of oligomycin (State 4o), and FCCP-induced maximal uncoupler-stimulated respiration (State 3u) were sequentially measured. The normalized data are expressed as pmol of O2 per minute or milli-pH units (mpH) per minute, per µg total protein. The dual-ATP production rate was assessed using Seahorse XFe24 Analyzer (Agilent Technologies, Santa Clara, CA, USA); simultaneous reads of ATP production from glycolysis and mitochondria were performed using a label-free technology XF Real-Time ATP Rate Assay kit, as described in the User Guide (Agilent Technologies).
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2

Metabolic Profiling of Wound Tissue and Cells

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Basal OCR, extracellular acidification rate (ECAR), and ATP production rate were measured using XF Cell Mito Stress Test kit, XF Glycolytic Rate Assay kit, and XF Real-Time ATP Rate Assay kit on Seahorse XF Analyzer (Agilent Technologies). The sensor cartridges used for measuring the oxygen flux was equilibrated in an XF Calibrant (Agilent Technologies) for 16–24 h before the experiment in a 0%-CO2 37 °C incubator. The granulation tissue from the wounds taken from mice after 8 days of wounding was carefully dissected and rinsed with unbuffered Krebs-Henseleit buffer (KHB) media. The tissue was placed at the bottom of the XF24 Islet Capture Microplate (Agilent technologies) and covered with a mesh. Four hundred and fifty microliters KHB medium was added to each well containing the tissue and equilibrated in a 0%-CO2 incubator for 30 min. The cartridge was then placed on the assay plate and run in the XF analyzer using an optimized protocol to measure basal OCR. For analysis in cells, HDFs were transfected with negative control mimic or miR-210 mimic and treated with normal (5.5 mM) or high (30 mM) glucose levels in normoxia or hypoxia. The cells from each condition were then seeded onto an XF24 or XFe96 Cell Culture Microplate and (Agilent Technologies). The results were normalized to protein concentration or cell number as indicated.
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3

Mitochondrial ATP Production Assay

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For ATP production rate assay an Agilent Seahorse XF Real-Time ATP Rate Assay Kit was used and HEK293 MUL1(−/−) and HEK293 MUL1(+/+) cells were plated as described above and ATP measurements were recorded followed by Oligomycin injection in port A (56 µl) at 1.5 μM final concentration, and Rotenone/Antimycin injection in port B (62 μl) at 0.5 μM final concentration. Data analysis was performed using Report Generators software for Real-Time ATP Rate Assay.
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4

Measuring Real-Time ATP Production in Human Astrocytes

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Human astrocytes (5 × 104 cells/well) were plated into XF96 cell culture microplates (101085-004, Agilent Technologies) and treated with indicated compound. Real-Time ATP production rate was measured with Seahorse XF96e bioanalyzer using XF Real-Time ATP Rate Assay Kit (103592-100, Agilent Technologies, Inc.) according to the manufacturer’s instructions. OCR levels in cells that were treated with oligomycin (2 μM), rotenone (10 μM), and antimycin (10 μM) were monitored and measured.
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5

Quantifying Mitochondrial ATP Production

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Percent ATP produced by mitochondria and the level of compensatory glycolysis were measured using a Seahorse XF Real-Time ATP Rate Assay Kit and XFe96 Analyzers (Agilent) according to manufacturer instructions. Seahorse XF Analyzers directly measure real time extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) of cells. ECAR and OCR are indicators of the two major energy-producing pathways: glycolysis and oxidative phosphorylation. Basal OCR and ECAR rates were first measured. Injection of oligomycin results in an inhibition of mitochondrial ATP synthesis that results in a decrease in OCR, allowing for quantification of mitochondrial ATP Production Rate. ECAR data combined with the buffer factor of the assay medium allows calculation of total Proton Efflux Rate (PER) using the following formula: PER (pmol H + /min) = ECAR (mpH/min) × BF (mmol/L/pH) × Geometric Volume (μL) × Kvol. Complete inhibition of mitochondrial respiration with rotenone plus antimycin A accounts for mitochondrial-associated acidification, and when combined with PER data allows calculation of the glycolytic ATP Production Rate. Compensatory glycolysis was measured as ATP production with complete inhibition of mitochondrial respiration.
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6

ATP Production Rate Assay in Cell Lines

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For ATP production rate assay an Agilent Seahorse XF Real-Time ATP Rate Assay Kit was used and HEK293 WT, HEK293 UBXN7(−/−), as well as HEK293 MUL1(−/−) cells were plated as described above and ATP measurements were recorded followed by Oligomycin injection in port A (56 μl) at 1.5 μM final concentration, and Rotenone/Antimycin injection in port B (62 μl) at 0.5 μM final concentration. Data analysis was performed using Report Generators software for Real-Time ATP Rate Assay.
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7

Measuring Mitochondrial ATP Production in Astrocytes

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For the mitochondrial ATP production assay, human astrocytes (5 × 104 cells/well) were plated on XF96 cell culture microplates (101085-004, Agilent Technologies, Inc., Santa Clara, CA, USA). Real-Time ATP production rate was measured by a Seahorse XF96e bioanalyzer using the XF Real-Time ATP Rate Assay Kit (103592-100, Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer's instructions. The OCR levels were monitored and measured in cells that were treated with oligomycin (2 μM), rotenone (10 μM) and antimycin (10 μM).
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8

Bioenergetic Analysis of Endothelial Cells

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Bioenergetic analysis in intact ECs was performed on a Seahorse XFe96 analyzer (Agilent Technologies, Santa Clara, CA, USA) using an XF Real-Time ATP Rate Assay Kit (103592-100, Agilent Technologies). Briefly, cells were seeded in the Seahorse XF96 cell culture microplates at 1 × 104 cells/well/80 µL and placed back in 37 °C, 5% CO2 incubator. After 24 h, cells were washed in assay media made up of Seahorse XF DMEM Medium, pH = 7.4 (103576-100, Agilent Technologies) containing 10 mM glucose, 1 mM pyruvate, and 2 mM L-glutamine and incubated for 1 h in a non-CO2 incubator at 37 °C before a final wash in the assay media. The Seahorse XFe96 analyzer was calibrated and the assay was run using a standard XF Real-Time ATP Rate template created using the WAVE Software (V2.6.1, Agilent Technologies) and assay standard drug injections were used of 1.5 µM oligomycin in port A and 0.5 µM rotenone/antimycin A in port B.
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9

Measuring Cellular Energy Metabolism

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Glycolytic and mitochondrial ATP production was measured with a Seahorse XFe96 Extracellular Flux Analyzer with an XF Real-Time ATP Rate Assay Kit (Agilent Technologies). Fibroblasts were seeded at 40,000 cells per well in complete DMEM and grown overnight in a 37 °C/5% CO2 incubator. Growth medium was removed and fibroblasts were treated with REN001 in complete DMEM for 48 h. Cells were washed twice with Seahorse XF Aassy Media and incubated for 1 h at 37 °C in a non-CO2 incubator in buffered Seahorse XF Assay Media (Agilent Technologies) supplemented with 1 mM sodium pyruvate, 2 mM L-glutamine, and 10 mM D-glucose. Manufacturer’s directions were otherwise followed for the Real-Time ATP Rate Assay Kit (Agilent Technologies).
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