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18 protocols using mem non essential amino acids

1

Maintenance of Human iPSC Lines

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The TkDN4-M (4M) hiPSCs line was a kind gift from Dr. M Ohtsu at The Institute of Medical Science, The University of Tokyo. 4M cells were cultured as previously described with minor modifications [23 (link)]. They were maintained on mitomycin C (MMC; FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan)-treated SNL feeder cells in hiPSCs medium (DMEM/Ham`s F12 (FUJIFILM Wako) supplemented with 20% Knockout Serum Replacement (KSR; GIBCO BRL, Palo Alto, CA, USA), 1x MEM nonessential amino acids (FUJIFILM Wako), 0.5x penicillin streptomycin(PS; FUJIFILM Wako), 55μM 2-melcaptoethanol (2ME Gibco) and 7.5μg/ml basic fibroblast growth factor (FGF2; Peprotech, Rocky Hill, NJ, USA). For passage, 4M colonies were detached using CTK solution, chipped by pipetting, and seeded onto MMC-treated SNL feeder (ECACC, Salisbury, UK) in hiPSCs medium once a week. The 15M63 hiPSCs line was kindly provided from the Center for iPS Cell Research and Application of Kyoto University (Kyoto, Japan) and maintained on vitronectin (Invitrogen, CA, USA) coated dishes in StemFit. For passage, 15M63 was dissociated with accutase (Innovative Cell Technologies, San Diego, USA) by pipetting and seeded on vitronectin coated dishes in StemFit (Ajinomoto, Tokyo, Japan) supplemented with 10μM Y27632 (Cayman Chemical, Ann Arbor, MI, USA).
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2

Culturing Nalm-6 Pre-B Cells

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Nalm-6 cells were cultured in a 5% CO2 incubator at 37 °C in MEM medium (Nissui Seiyaku) supplemented with 10% calf serum (Hyclone), 2 mM MEM non-essential amino acids (Wako Pure Chemical), 1 mM sodium pyruvate (Wako Pure Chemical), 50 μM 2-mercaptoethanol (Wako Pure Chemical) and 0.15 μM Vitamin B12 (Sigma-Aldrich). Nalm-6 is a human pre-B cell line available from ATCC and was kindly provided by Dr Michael R. Lieber. The Nalm-6 cell line was originally established from the peripheral blood of a 19-year-old man with acute lymphoblastic leukaemia59 (link) and has a stable near-diploid karyotype60 (link). All cell lines used in this study are not listed in the database of commonly misidentified cell lines maintained by ICLAC and were tested for mycoplasma contamination using an e-Myco Mycoplasma PCR Detection Kit (iNtRON Biotechnology, Inc.).
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3

Culturing Mouse Embryonic Stem Cells

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In this study, we used mESC line E14tg2a (Riken Cell Bank, Japan).28 (link) mESCs were cultured at 37 °C and 5% CO2 on cell culture dishes coated with 0.1% gelatin from porcine skin (gel strength 300, type A; Sigma-Aldrich, USA). The cells were maintained with Glasgow Minimum Essential Medium (G-MEM; Wako, Japan) with 15% fetal bovine serum (FBS) (Sigma-Aldrich), 1 mmol/L sodium pyruvate (Wako), 1% MEM non-essential amino acids (Wako), 0.1 mmol/l 2-mercaptoethanol (Wako), and 1000 units/ml LIF (Wako). The cells were dissociated by TrypLE Express (Thermo Fisher Scientific, USA) and passaged at 7.0 × 103 cells/cm2 for 2-Day interval passage or 2.6 × 103 cells/cm2 for 3-Day interval passage.
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4

Culturing HepG2 Cells for Biochemical Assays

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HepG2 cells (RCB1648) purchased from Riken Cell Bank (Tsukuba, Japan) were maintained in Minimum Essential Medium Eagle (MEM, FUJIFILM Wako) containing 10% fetal bovine serum (FBS, Thermo Fisher Scientific Inc., Waltham, MA, USA), 1% MEM nonessential amino acids (FUJIFILM Wako), 100 units/mL penicillin G, and 100 μg/mL streptomycin (FUJIFILM Wako) at 37 °C under a humidified atmosphere containing 5% CO2. Each sample was prepared in DMSO to achieve a final concentration of 0.5%.
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5

Infection Assay of E. coli K1 in HBMECs

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HBMECs were cultured in RPMI 1640 medium (Thermo Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS, Hyclone, Marlborough, MA, USA), 10% Nu-serum (BD Biosciences, Franklin Lakes, NJ, USA), 2 mM glutamine, 1% MEM nonessential amino acids (Wako, Osaka, Japan), 1 × MEM vitamin (Sigma, Irvine, UK), 100 U/mL penicillin, 100 μg/mL streptomycin, and 1 mM sodium pyruvate (Thermo Scientific). E. coli K1 strains were resuscitated from −80 °C, cultured overnight, and then subcultured in fresh BHI medium at a dilution of 1:100 until strains were grown to the exponential phase at an OD600 of 0.6. Bacteria were collected by centrifugation and resuspended in RPMI 1640 medium containing 10% FBS. HBMECs infected at a multiplicity of infection (MOI) of 100 were incubated for 1.5 h in a cell incubator. The HBMECs were then washed with phosphate-buffered saline (PBS) to remove unbound bacteria and incubated with new medium containing gentamicin (100 mg/mL) for 1 h to kill extracellular E. coli. HBMECs were washed, lysed with 0.5% triton X-100, and plated on Luria broth (LB) agar plates for the determination of CFUs. A binding assay was performed similarly to the invasion assay except that the gentamicin treatment step was omitted. All experiments were conducted in duplicate and performed at least in triplicates.
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6

Maintaining HepG2 Cell Culture

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HepG2 cells (RCB1648, Riken Cell Bank, Tsukuba, Japan) were maintained in Minimum Essential Medium Eagle (MEM, Sigma-Aldrich Co. LLC., St. Louis, MO, USA) containing 10% fetal bovine serum, 1% MEM non-essential amino acids (FUJIFILM Wako Pure Chemical Corporation, Tokyo, Japan), penicillin G (100 units/mL), and streptomycin (100 µg/mL) at 37 °C under 5% CO2 atmosphere.
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7

Human iPS Cell Line Maintenance

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The human iPS cell line (TkDN4-M: 4M) was a kind gift from Dr. M. Ohtsu at The Institute of Medical Science, University of Tokyo. Undifferentiated 4M were maintained on mitomycin C (MMC; FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan)-treated SNL feeder cells in human iPS cell medium (DMEM/Ham's F12 (FUJIFILM Wako) supplemented with 20% Knockout Serum Replacement (KSR; GIBCO BRL, Palo Alto, CA, USA), 1x MEM nonessential amino acids (FUJIFILM Wako), 0.5x penicillin streptomycin (PS; FUJIFILM Wako), 55 μM 2-melcaptoethanol (2 ME Gibco) and 7.5 μg/ml basic fibroblast growth factor (FGF2; Peprotech, Rocky Hill, NJ, USA). For passage, 4M colonies were detached with CTK solution, dissociated into single cells, and seeded onto MMC-treated SNL feeder (ECACC, Salisbury, UK) in human iPS cell medium once a week.
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8

Culturing C57BL/6 mESCs in 2i Conditions

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Bruce 4 C57BL/6 mESCs (Merk Millipore, Billerica, MA) (and later derivatives) were cultured in 2i conditions (StemSure D-MEM [Wako Pure Chemicals, Osaka, Japan], 15% fetal bovine serum, 0.1 mM β-mercaptoethanol, 1 × MEM nonessential amino acids [Wako Pure Chemicals], 2 mM l-alanyl-l-glutamine solution [Wako Pure Chemicals], 1000 U/mL LIF [Wako Pure Chemicals], 20 µg/mL gentamicin [Wako Pure Chemicals], 3 µM CHIR99021, and 1 µM PD0325901) on a 0.1% gelatin-coated dish. Before each experiment, cells were passaged two times and cultured in 2i conditions as well as serum conditions (StemSure D-MEM, 15% fetal bovine serum, 0.1 mM β-mercaptoethanol, 1 × MEM nonessential amino acids, 2 mM l-alanyl-l-glutamine solution, 1000 U/mL LIF, 20 µg/mL gentamicin), or in serum conditions containing 2i inhibitors or PD0325901 at several concentrations, as described in Supplementary Table S1. TSA and 5-AzaC were added to the cells at a final concentration of 50 nM and 50 μM, respectively. They were applied for 72 hours.
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9

Culturing Undifferentiated Calu-6 Lung Cancer Cells

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The undifferentiated human lung cancer cell line Calu-6 (ATCC, Manassas, VA, USA) was used. Calu-6 cells were cultured in Eagle’s minimal essential (EMEM) medium (Fujifilm Wako Pure Chemical Industries, Osaka, Japan) supplemented with 10% FBS, MEM non-essential amino acids (Fujifilm Wako Pure Chemical Industries, Osaka, Japan), 1 mM sodium pyruvate (Fujifilm Wako Pure Chemical Industries), and 0.1% penicillin-streptomycin (Life Technology Co., New York, NY, USA) under 5% CO2 at 37 °C.
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10

Cytokine Production in Immune Cells

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DC2.4 cells, an immature DC cell line, were cultured in RPMI 1640 culture medium (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 0.05 mM 2-mercaptoethanol, 10 mM HEPES, 1 mM sodium pyruvate, 100 μM minimal essential medium (MEM) non-essential amino acids, 100 U/mL of penicillin, and 100 μg/mL of streptomycin (Wako). RAW 264.7 cells, a mouse macrophage cell line, were cultured in Dulbecco’s modified Eagle medium supplemented with 10% heat-inactivated fetal bovine serum, 100 μM MEM non-essential amino acids (Sigma–Aldrich), 100 U/mL of penicillin, and 100 μg/mL of streptomycin (Sigma–Aldrich). DC2.4 cells (5 × 104 cells) and RAW 264.7 cells (5 × 104 cells) were seeded in 96-well culture plates, respectively, and incubated to adhere overnight at 37°C in a humidified atmosphere of 5% CO2. After the incubation, the cells were treated with 10 μg/mL LH2171 and incubated for a further 4 h. Then, DC2.4 cells were stimulated with LPS from Escherichia coli 055:H5 (Sigma–Aldrich) at a final concentration of 1 μg/mL, and RAW 264.7 cells were stimulated with LPS from E. coli 0111:B4 (Sigma–Aldrich) at a final concentration of 10 μg/mL for 20 h. In all experiments, the cells were grown to 80–90% confluence.
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