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4 protocols using penicillin streptomycin

1

Tracing Metabolic Dynamics in Cell Activation

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For tracing experiments, MDSC + ISO and MDSC + PBS in one set and β2-AR-/- + ISO and β2-AR-/- + PBS in another set were generated using rmIL-6 and rmGM-CSF (40 ng/mL each) for 4 days. On day 4, the cells were incubated with tracing media: Gln-free RPMI medium supplemented with 10% dialyzed FBS (Life Technologies), 20 mM HEPES, 0.05 mM 2-mercaptoethanol, and 1% penicillin-streptomycin plus 2 mM 13C5-glutamine (13C5-Gln) (Cambridge Isotope Laboratories,). At 2 h, 8 h. and 24 h. incubation timepoints, the cells were washed twice with PBS, once quickly with distilled water, and quenched with 60% cold acetonitrile in water. Polar metabolites were extracted by the solvent partitioning method with a final CH3CN:H2O:CHCl3 (2:1.5:1, v/v) ratio, followed by a second extraction including methanol, and lyophilized as previously described73 (link),74 .
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2

Gln-dependent Mouse HCC Cell Line

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Gln-dependent mouse HCC cell line (EC4) cells were obtained from Dr. Dean Felsher and cultured in Dulbecco Modified Eagle Medium (DMEM) (Corning) supplemented with 10% fetal bovine serum (FBS, Sigma) and 1% penicillin-streptomycin (Corning). For SIRM analysis, these cells were cultured in glutamine (Gln)-free DMEM (Thermo Fisher Scientific, catalogue # A1443001), 10% dialyzed FBS (cat# 26-400-044, GIBCO), 1% penicillin-streptomycin, and 3 mM [U–13C,15N]-Gln (Cambridge Isotope Laboratories). For ectopic miR-122 expression, these cells were transfected with 50 nM of miR-122 mimic (Dharmacon Catalogue# C-300591-05) or negative control mimic (Dharmacon, Catalogue# CN-001000-01-50) using RNAimax (Invitrogen) following the manufacturer's protocol. Hepa1-6 cell line obtained from Dr. Gretchen Darlington was grown in the same media containing regular Gln.
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3

Quantitative Proteomics of Epigenetic Regulation

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NCI-H1299 cells were cultured as described above, and DAC was administered for 72 h and SB939 for 18 h for the whole duration of depletion and labeling. The media containing the inhibitors was refreshed every 24 h. For the AHA pulse, SILAC labeling cells were depleted of methionine, lysine, and arginine for 30 min by using RPMI medium 1640 non-GMP formulation (ThermoFisher Scientific, Waltham, USA) devoid of the aforementioned amino acids, supplemented with 10% dialyzed FBS (ThermoFisher Scientific) and 50 U/ml Penicillin–Streptomycin (ThermoFisher Scientific). After depletion, cells were labeled with RPMI medium 1640 non-GMP formulation supplemented with 0.1 mM L-AHA (AnaSpec, Inc), [13C6, 15N4] L-arginine, and [13C, 15N2] l-lysine for heavy isotope labeling or supplemented with 0.1 mM L-AHA), [13C6] L-arginine and [4,4,5,5-D4] L-lysine (Cambridge Isotope Laboratories, Inc., Tewksbury, USA) for intermediate isotope labeling for 4 h. Both labeling media were supplemented with 10% dialyzed FBS and 50 U/ml Penicillin–Streptomycin. Cells were washed three times with PBS and detached by scraping, then centrifuged for 5 min at 1000 × g. PBS was discarded and cell pellets were frozen at −80 °C or immediately subjected to protein extraction and enrichment.
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4

CFTR Mutant Cell Line Culture

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CFBE41o- and WT-HBE41o- bronchial epithelial cell lines, which express ΔF508 or wild-type CFTR, respectively, as well as FRT cells expressing either wild-type, ΔF508, N1303K, G551D or R117H CFTR were kindly provided by Dr. J. Clancy (University of Alabama, Birmingham, AL) (66 (link)). The CFBE41o- cell line was derived from a CF patient homozygous for ΔF508, whereas the wild-type cell line (HBE) was generated from CFBE41o- cells by re-introduction of F508 using SFHR (67 (link)). CFBE41o- and WT-HBE41o- cells were cultured at 37 °C, 5% CO2 in Advanced- MEM (GIBCO, Carlsbad, CA) supplemented with 1% Penicillin/Streptomycin (GIBCO), 10% fetal bovine serum (GIBCO) and 2 mM L-Glutamine (GIBCO) and appropriate selective antibiotics. For SILAC labeling experiments, cells were cultured for > 6 passages in lysine and arginine free SILAC-A-MEM (Gibco, custom media), supplemented with heavy-labeled 13C615N2 Lysine and 13C615N4 Arginine (Cambridge Isotope Laboratories, Tewksbury, MA), 2% FBS, 1% Penicillin/Streptomycin, and 2 mM L-Glutamine. FRT cells were cultured at 37 °C, 5% CO2 in Ham’s F12, Coon’s modification (Sigma-Aldrich) supplemented with 5% FBS and 100 μ/ml hygromycin (Invitrogen). Treatment with 5 – 10 μM VX809 (Selleck, Houston, TX), 10 μM CX-4945 (Santa Cruz Biotechnologies, Dallas, TX) or vehicle (DMSO), was carried out for 20 hours or as indicated.
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