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4 protocols using 2 3 3 2h serine

1

Metabolomic Analysis of Cell Lines

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FBS, penicillin, and streptomycin were purchased from HyClone Laboratories. RPMI 1640 medium and charcoal-stripped FBS were purchased from Thermo Fisher. Dialyzed FBS was from Life Technologies. Optima ammonium acetate, ammonium hydroxide, Optima liquid chromatography–mass spectrometry (LC-MS) grade, acetonitrile, methanol, and water were purchased from Fisher Scientific. U-13C glucose, U-13C glutamine, and 2,3,3-2H serine were obtained from Cambridge Isotope Laboratories. U-13C palmitate, C16-ceramide, and C2-ceramide were purchased from Sigma-Aldrich.
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2

Metabolomic Analysis of Cell Lines

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FBS, penicillin, and streptomycin were purchased from HyClone Laboratories. RPMI 1640 medium and charcoal-stripped FBS were purchased from Thermo Fisher. Dialyzed FBS was from Life Technologies. Optima ammonium acetate, ammonium hydroxide, Optima liquid chromatography–mass spectrometry (LC-MS) grade, acetonitrile, methanol, and water were purchased from Fisher Scientific. U-13C glucose, U-13C glutamine, and 2,3,3-2H serine were obtained from Cambridge Isotope Laboratories. U-13C palmitate, C16-ceramide, and C2-ceramide were purchased from Sigma-Aldrich.
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3

Tracing Serine Metabolism in Cells

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Experiments with [U-13C]-serine and [2,3,3-2H]-serine (Cambridge Isotope Laboratories) were performed in customized serine-, glycine- and glutamine-free RPMI-1640 (Cell Culture Technologies, Switzerland) with 0.4 mM glycine, 2 mM glutamine, 0.4 mM serine tracer and 10% FBS (or dFBS). Then 200,000 cells were seeded in 500 μl medium in 24-well plates in triplicates for each condition and in parallel triplicates for cell count and volume determination (to calculate the packed cell volume (PCV)). The day after, medium was replaced by 500 μl tracer medium with and without treatment. Three untreated wells per cell line were counted for start PCV. After 24 h of culture, one set of triplicate wells per condition were counted for end PCV. A parallel set of triplicate wells was used to collect medium for formate release rates and to preform metabolite extraction for liquid chromatography–mass spectrometry (LC–MS) analysis.
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4

Isotopic Tracer Preparation for Cell Culture

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The following isotopic tracers were purchased from the indicated sources: [2,3,3-2H]serine, [1-2H]glucose, [3-2H]glucose, [U-13C]glutamine and [U-13C]glucose (Cambridge Isotope Laboratories) and [2,2,3,3-2H]dimethyl succinate (Sigma-Aldrich). Isotope-labeled glucose and glutamine medium was prepared from phenol red–, glucose-, glutamine-, sodium pyruvate–, sodium bicarbonate–free DMEM powder (Cellgro) supplemented with 3.7 g/L sodium bicarbonate, 25 mM glucose and 4 mM glutamine. Isotope-labeled serine medium was prepared from scratch following the standard DMEM formula, by mixing together stock solutions containing vitamins, amino acids without serine, inorganic salts, and glucose, and thereafter supplemented with 42 mg/L [2,3,3-2H]serine. Isotope-labeled succinate medium was prepared from DMEM powder, 25 mM glucose, 4 mM glutamine supplemented with 2 mM [2,2,3,3-2H]dimethyl succinate. In HEK293T cells (but not the 3T3-L1 cells studied here) decreasing the glucose and glutamine levels in DMEM to 10 mM and 1 mM, respectively, increases fractional malate labeling from the tracer and thereby facilitates malic enzyme flux measurement. Isotopic medium was supplemented with 10% dialyzed FBS (Sigma-Aldrich) and, for differentiating cells only, 5 μg/ml insulin.
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