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14 protocols using mem vitamins

1

Isolation and Culture of Endothelial Cells

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Bovine aortic endothelial cells (BAECs) were isolated as previously described45 (link), and cultured in medium 199 (M-199) (Gibco) supplemented with 100 U/mL of penicillin and 100 μg/mL of streptomycin (Gibco), 1% MEM amino acids (Gibco), 1% MEM vitamins (Cellgro), 10% fetal clone III (bovine serum product, HyClone), at 37 °C with 5% CO2. Cells at passages 5 to 8 were used for experiments. Human umbilical vein endothelial cells (HUVECs) were isolated and maintained in Medium 200 (Cascade Biologics) with low serum growth supplements. Cells at passages 2 to 4 were used. To reduce the background signals of kinases, cells were cultured for one day in serum free medium prior to the flow experiments (shear stress of 12 dyn/cm2) using a cone and plate viscometer. The cells were handled according to the regulations of the Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences, Beijing, China, and the study protocol was approved by the Institutional Review Board of the Institute of Basic Medical Sciences, the Chinese Academy of Medical Sciences. Written informed consent was obtained either from the donor or a close relative for HUVEC isolation.
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2

Culturing Human Uveal Melanoma Cell Lines

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All cell lines were cultured at 37 °C, 5% CO2 in a humidified incubator according to the standard protocol of mammalian cell culturing. Human UM cells 92.1, OCM1, OMM2.3, OMM3, M20-07-070, M20-09-196, Mel290, and Mel270, authenticated by STR (Emory Genomics core facility) [22 (link)] were cultured in RPMI 1640 with L-glutamine (Corning Cellgro, Albany, NY) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO), Sodium Pyruvate (Cellgro, Albany, NY), MEM Non-Essential Amino Acids (Cellgro, Albany, NY), MEM Vitamins (Cellgro, Albany, NY), Penicillin-Streptomycin Solution (Cellgro, Albany, NY), and HEPES buffer (Corning, Albany, NY). The 92.1 and OMM2.3 cells were provided by Dr. Jerry Niederkorn (Department of Ophthalmology, UT Southwestern, Dallas, TX). The Mel290 and Mel270 cells were provided by Dr. Bruce Ksander (Schepens Eye Institute, Boston, MA). The OCM1 and OMM3 cells were donated by Dr. June Kan-Mitchel (Wayne State University, Detroit, MI). Dr. Scott Woodman (Department of Melanoma Medical Oncology and Systems Biology, MD Anderson Cancer Center, Houston, TX), Dr. Barry Burgess, and Dr. Tara McCannel (UCLA, Jules Stein Eye Institute, Calabasas, CA) isolated and provided M20-09-196 and M20-07-070 cell lines. SKOV3 ovarian cancer cells were cultured in McCoy 5 A medium with 10% fetal bovine serum and 1% penicillin and streptomycin.
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3

Quantification of SARS-CoV-2 Spike Protein Binding to ACE2

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Human codon-optimized SARS-CoV-2 spike-protein sequence was synthesized by MolecularCloud (MC_0101081). 5′-ACGACGGAATTCATGTTCGTCTTCCTGGTCCTG-3′ and 5′-ACGACGGAATTCTTAACAGCAGGAGCCACAGC-3′ primers were used to amplify the SARS-CoV-2 spike protein sequence without ERRS that is the last 19 amino acids33 (link). Full length and truncated SARS-CoV-2 spike-protein sequences were then cloned into pLP/VSVG plasmid from Thermo Fisher under CMV promoter after removing the VSVG sequence via EcoRI-EcoRI restriction digestion. HEK-293T cells (ATCC; mycoplasma-free low passage stock) were transfected with the expression plasmids using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s protocol. The cells were cultured in complete RPMI 1640 medium (RPMI 1640 supplemented with 10% FBS; Atlanta Biologicals, Lawrenceville, GA), 8% GlutaMAX (Life Technologies), 8% sodium pyruvate, 8% MEM vitamins, 8% MEM nonessential amino acid, and 1% penicillin/streptomycin (all from Corning Cellgro) for 72 h46 (link). The cells were then collected using %0.05 Trypsin-0.53 mM EDTA (Corning Cellgro) and stained with Biotinylated Human ACE2/ACEH Protein, Fc,Avitag (Acro Biosystems) then stained with APC anti-human IgG Fc Antibody clone HP6017 (Biolegend). Samples were acquired on a BD FACSymphony A5 analyzer and data were analyzed using FlowJo (Tree Star).
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4

Recombinant E1FTL→TVG Protein Expression

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The vector encoding His6-E1FTL➔TVG was transformed into BL21(DE3) CodonPlus RP competent cells using a heat-shock technique, and the cells were plated on agar with the appropriate antibiotics overnight at 37C. Single colonies were picked and added to LB medium with appropriate antibiotics then agitated at 37C for 6–8 hours or until solutions were turbid. 2–3 mL of this starter culture was added to 1L of 15N-M9 media (0.1 mM CaCl2, 1 mM MgSO4, 0.4% glucose, 10 mL 1X MEM vitamins from Corning Cellgro, 100ug/ml of ampicillin, and 34 ug/ml of chloramphenicol). This was followed by rotary shaking at 25C for 16–18 hours until the optical density (OD600) was between 0.7 and 1.0. Cell expression was induced using 1 mM IPTG, followed by continued rotary shaking at 37C for 6 hours. The cells expressing recombinant E1FTL➔TVG were harvested at 4C at 6,000 X g, flash frozen, and stored at −80C until ready for purification.
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5

Authenticated Human Uveal Melanoma Cell Culture

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All cell lines were cultured at 37°C, 5% CO2 in a humidified incubator according to the standard protocol of mammalian cell culturing. Human UM cells 92.1, OCM1, OMM2.3, OMM3, M20–07-070, M20–09-196, Mel290, and Mel270, authenticated by STR (Emory Genomics core facility) 22 (link) were cultured in RPMI 1640 with L-glutamine (Corning Cellgro, Albany, NY) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO), Sodium Pyruvate (Cellgro, Albany, NY), MEM Non-Essential Amino Acids (Cellgro, Albany, NY), MEM Vitamins (Cellgro, Albany, NY), Penicillin-Streptomycin Solution (Cellgro, Albany, NY), and HEPES buffer (Corning, Albany, NY). The 92.1 and OMM2.3 cells were provided by Dr. Jerry Niederkorn (Department of Ophthalmology, UT Southwestern, Dallas, TX). The Mel290 and Mel270 cells were provided by Dr. Bruce Ksander (Schepens Eye Institute, Boston, MA). The OCM1 and OMM3 cells were donated by Dr. June Kan-Mitchel (Wayne State University, Detroit, MI). Dr. Scott Woodman (Department of Melanoma Medical Oncology and Systems Biology, MD Anderson Cancer Center, Houston, TX), Dr. Barry Burgess, and Dr. Tara McCannel (UCLA, Jules Stein Eye Institute, Calabasas, CA) isolated and provided M20–09-196 and M20–07-070 cell lines. SKOV3 ovarian cancer cells were cultured in McCoy 5A medium with 10% fetal bovine serum and 1% penicillin and streptomycin.
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6

Isolation and Characterization of T Cell Subsets

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Peripheral blood mononuclear cells from healthy individuals (New York Blood Center, New York, NY) were prepared using Ficoll-paque plus (GE Healthcare). CD4+ T cells and CD8+ T cells were isolated using Dynal CD4 Positive and CD8 Positive Isolation Kit (Invitrogen) respectively, and were >99% pure. Purified CD4+ cells were sorted in some experiments by flow cytometry (FACSAria; BD Biosciences) based on CD45RO, CCR7, CD25 and chemokine receptors expression into: 1) Naïve T cells (CD45RO CCR7+CD25), 2) Memory T cells (CD45RO+CD25), 3) Naïve Tregs (CD45RO CD25+) and 4), Th1 cells (CD45RO+CCR6CCR4CXCR3+), 5) Th2 cells (CD45RO+CCR6CCR4+CXCR3) and 6) Th17 cells (CD45RO+CCR6+). Sorted subsets were >98% pure and were kept at 37°C and 5% CO2 in complete RPMI 1640 medium (RPMI supplemented with 10% Fetal Bovine Serum (FBS, Atlanta Biologicals, Lawrenceville, GA), 8% GlutaMax (Life Technologies), 8% sodium pyruvate, 8% MEM Vitamins, 8% MEM Nonessential Amino acid and 1% penicillin/Streptomycin (all from Corning Cellgro).
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7

Hypoxia Regulation of Ovarian Cancer

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OvCa cells were maintained in standard DMEM supplemented with 10% FB-Essence (VWR Life Science SeraDigm, Radnor, PA) with 1% penicillin/streptomycin (Corning, Corning, NY), 1% MEM non-essential amino acids (Corning) and 1% MEM vitamins (Corning). All cell lines were genotyped to confirm their authenticity (IDEXX Bioresearch short tandem repeat marker profiling every 3 months), and were used between 2-12 passages from first thaw. All experiments were carried out in low glucose DMEM (VWR Life Science) supplemented as above. The pLX304 SPHK1-V5 lentiviral expression vector was purchased from DNASU (Tempe, AZ). The constitutively active HIF1α (P402A/P564A) and HIF2α (P405A/P531A) plasmids were a gift from William Kaelin (27 (link)) obtained through Addgene (Cambridge, MA). 5HRE-GFP reporter was a gift from Martin Brown and Thomas Foster obtained through Addgene (28 (link)). SPHK1 siRNA was obtained from GE Dharmacon (Lafayette, CO). Metformin, phenformin, CoCl2, and thiazolyl blue tetrazolium bromide were purchased from Sigma Aldrich (St. Louis, MO). S1P (Huzzah S1P) was purchased from Avanti Polar Lipids (Alabaster, AL). Hypoxia was induced through 1% O2/5% CO2 using Hypoxia Incubator Chamber by STEMCELL Technologies (Vancouver, BC, Canada).
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8

Cell Culture Media Preparation Protocol

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Dulbecco's Modified Eagle's Medium (DMEM) (Catalogue # 10-013-CV), MEM vitamins (Catalogue # 25-020-CI), MEM nonessential amino acids (Catalogue # 25-025-CI), Penicillin-Streptomycin (Catalogue # 30-002-CI) and trypsin (Catalogue # 25-053-CI) were purchased from Corning. FBS was purchased from Gibco (LifeTechnologies, catalogue # 16000-044). Giemsa stain (Catalogue # GS500) and crystal violet (Catalogue # C0775) were obtained from Sigma Aldrich. Thiazolyl blue tetrazolium bromide was from Acros Organics (Catalogue # 298-93-1) and 4% paraformaldehyde solution was purchased from Fisher Scientific (NC9245948).
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9

Cell Line Culture and Maintenance Protocol

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HeLa, PC3, LNCaP, SKOV3, MCF7, and U87 and OVCAR3 cell lines were obtained from ATCC and were not STR profiled. Cell lines have been tested for mycoplasma contamination. HeLa, LNCaP, PC3, SKOV3, MCF7, and U87 cells were cultured in RPMI 1640 (Hyclone, #SH30027.01) supplemented with 10% fetal bovine serum (FBS, Atlanta Biologicals, #912850) and 1% Penicillin/Streptomycin (Hyclone, #SV30010). OVCAR3 and PC3 cells were cultured in DMEM (Hyclone, #SH30243.01) supplemented with 10% FBS, 1% Penicillin/Streptomycin, 1% MEM nonessential amino acids (Corning, #25-025-CI), and 1% MEM vitamins (Corning, #25-020-CI). All cell lines were grown at 37 °C in a 5% CO2 humidified incubator.
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10

Ovarian Cancer Conditioned Media Effects

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To generate OvCa conditioned media (CM) for treatment of HPMCs, TYKnu cells were plated on 10cm dishes at 1,000,000 cells per plate and allowed to grow for 24h in standard growth media. Media was then replaced with low glucose DMEM (supplemented with 10% FB-Essence, 1% pen/strep, 1% MEM non-essential amino acids and 1% MEM vitamins; Corning) and cells were allowed to grow for 72h prior to collection. Media was centrifuged and moved to a new tube to avoid cell debris, and stored at −20°C until use. For analysis of mesothelial cells co-cultured with OvCa cells, HPMCs were plated at 300,000 cells per well on a 6-well plate and TYKnu cells were plated at 100,000 cells per transwell polyester membrane insert (0.4μm pore size, for use with 6-well plate; Corning) on a separate plate. Cells were cultured separately for 24h priorto moving inserts to co-culture TYKnu OvCa cells with HPMCs for 48h. Treatments for CM and co-culture experiments were performed as described in the figure legends. Conditioned media or transwell insert containing OvCa cells was then discarded and HPMCs were lysed and prepared for western blot or proteomics, as described below.
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