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13 protocols using dulbecco modified eagle medium (dmem)

1

Amino Acid Starvation in Breast Cancer

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The human breast cancer cell lines MCF-7, MDA-MB-231, and Hs 578T were cultured in DMEM (United States Biological) with 10% fetal bovine serum (FBS, Life Technologies), 1% penicillin/streptomycin (P/S), and 1% non-essential amino acids at 37°C and 5% CO2 in an incubator. The human breast cancer cell line HCC 1937 was cultured in RPMI 1640 (United States Biological) with 10% FBS and 1% P/S. To prepare the culture medium for each amino acid starvation condition, DMEM or RPMI 1640 medium without amino acids (D9800-13 and R9010-01, United States Biological) was mixed with different amino acid combinations lacking a specific amino acid (LAA21-1KT, Sigma-Aldrich).
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2

Glioblastoma and Breast Cancer Cell Lines

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All reagents not specified were purchased from Sigma (St. Louis, MO, USA). CBR-5884, a PHGDH inhibitor, and RA 839, a Nrf2 (nuclear factor erythroid 2-related factor) activator, were purchased from Tocris (Bristol, UK). LNT-229, LN-308, LN-428 and G55 cells have been described.35 (link) LNT-229 and LN-308 cells were a kind gift from N. de Tribolet (Lausanne, Switzerland), G55 cells were a kind gift from Manfred Westphal and Kathrin Lamszus (Hamburg), LN-428 cells and LN-464 cells were a kind gift from Monika Hegi (Lausanne). MDA-MB-231 and MDA-MB-464 cells were a kind gift from Winfried Wels (Frankfurt, Germany).
Wildtype cell lines were maintained as described.35 (link) For experiments glycine- and serine-free DMEM (US Biological Life Sciences, catalog no. D9800-03/D9802-01, Salem, MA, USA) was supplemented with glucose or serine as indicated. FCS included serine and its supplementation yielded serine concentrations of 20 µM (in comparison to 400 µM when serine was replenished). pLKO.1- and pTetOne-transfected cells were maintained in medium with 2 µg/ml puromycin. 0.1 µg/ml doxycycline was added to induce gene expression of PHGDH from pTetOne-transfected cells. To compare sub cell lines equal cell densities were confirmed by crystal violet (CV) staining as described.36 (link)
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3

Measuring Cell Soma Diameter in CRISPR Cells

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Cell soma diameter was measured in digital images of CRISPR-edited, scramble control, or WT N2aC lines in ImageJ (Schneider et al., 2012 (link)). Each measurement was taken using the longest dimension of each soma in 50 total cells (25 cells in 2 replicates). To define the mTOR dependency of cell size changes, cells were incubated with the mTOR inhibitor rapamycin (50 nM, 24hrs, Cell Signaling Technologies, Danvers, MA), torin1, a specific ATP-competitive dual kinase inhibitor of mTORC1 and mTORC2 (50 nM; 24 hrs; Torcris, Bristol, UK), or amino acid free (AAF) media (1 hr., DMEM, US Biological, Salem, MA) using DMSO as a vehicle control. Statistical analysis of cell size differences was assessed in Origin (Northampton, MA) using one-way ANOVA (p < 0.05 considered statistically significant). Measurements were graphed using a box and whisker plot where the box represents the standard error of the mean and the whiskers represent the 5–95% confidence interval.
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4

Cell Culture Conditions for Metabolic Studies

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Huh7, PLC/PRF/5 and HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) at 37 °C under 5% CO2 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin. All cells were obtained from the Bank of Type Culture Collection of Chinese Academy of Sciences, recently authenticated by fingerprinting of short tandem repeats, and tested negative for mycoplasma. For serine and glycine depletion, cells were cultured in serine- and glycine-free DMEM (US Biological Life Sciences, D9800-03) supplemented with 10% dialyzed FBS.
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5

Antibody Panel for Cellular Signaling

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Primary antibodies for Phospho-S6 Ribosomal Protein ser235/236, mTOR, phospho-4EBP1, and GAPDH were from Cell Signaling, Phospho-FAK (Tyr397), HPDL from Thermo Fisher, Paxilin and LAMP2 from BD-bioscience; PAK1 from Proteintech. Secondary antibodies Alexa-fluor 594 anti-Rabbit IgG, Alexa-fluor 488 anti-Rabbit IgG, Alexa-fluor 594 anti-Mouse IgG and Alexa-fluor 488 anti-Mouse IgG were from Cell Signaling, IRDye 800CW and IRDye 680CW were from LI-COR. Alexa fluor TM 555 Phalloidin, Click-iT EdU Imaging Kits, CellEvent Caspase-3/7 Green Detection kit, NHS-Fluorescein, NHS-Alexa Fluor 555, pH-rodo iFL STP ester red and Hoechst 33342 were from Invitrogen. DRAQ5 was from LI-COR. Collagen I and Matrigel were from Corning. Geltrex was from Thermo Fisher. All media and dialyzed FBS were from Gibco, except for DMEM with no amino acid which was from US Biological life science and Plasmax which was kindly provided by Dr Tardito, CRUK Scotland Institute, Glasgow. The details of Plasmax composition were previously described by Vande Voorde and colleagues [18 (link)]. E64d (Aloxistatin) and PF573228 were from AdooQ Bioscience. GM6001 was from APEXBIO. Dynasore, Filipin, and EIPA were from Sigma. FRAX 597 was from bio-Techne. Nitisinone was from MCE. PP2 was from Generon. C13-tyrosine was from Sigma-Aldrich.
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6

Amino Acid Combinations Influence Brown Adipocyte Respiration

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Mouse brown fat precursor cells were enzymatically isolated from iBAT of C57BL/6N male mice and differentiated in culture for 9 days as previously described (39 (link)). Primary brown adipocytes maintained in amino acid-free DMEM (USBiological Life Science, DBA, Milan, Italy) for 16 h, were pretreated with rapamycin (1.0 nmol/L) or vehicle (DMSO; Sigma-Aldrich) for 1 h and subsequently supplemented for a further 24 h with one of two different amino acid combinations, precisely reproducing the iBAT aminograms resulting from consumption of the SFA-CAA or SFA-EAA diet (Supplementary Table 4). Cellular oxygen consumption rates (OCRs) were determined using a Seahorse XF24 Extracellular Flux Analyzer (Agilent, Santa Clara, CA). Before analysis, the culture medium was changed to respiration medium. After basal respiration, uncoupled and maximal respiration was determined after the addition of oligomycin (1 μmol/L) and subsequently carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP, 0.2 μmol/L). Rotenone (3 μmol/L) was used to abolish mitochondrial respiration. All reagents were purchased from Sigma-Aldrich.
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7

HMEC-1 Cell Growth Assay

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HMEC-1 cells or HMEC-1 cells overexpressing xCT or SLC1A3 were seeded into 24-well plates (Greiner Bio-One) at a density of 6.5 x 103 cells per well in 0.5 mL medium. The following day, medium was changed to 1 mL HMEC-1 growth medium with any indicated supplements. For assays with added aspartate, medium was changed to custom DMEM medium without glucose, glutamine, or pantothenate (US Biological) supplemented with 5.55 mM glucose (Gibco), 1 mM pyruvate (Sigma), and 25 μM pantothenate (Sigma) along with supplements above: EGF, hydrocortisone, glutamine, HI-FBS. Media was buffered with sodium hydroxide to pH 7.95. Designated plates were placed in hypoxia chamber at 1% oxygen. Cell number was measured at the indicated time points using sulforhodamine B (Sigma) staining, as previously described [42 (link)]. Absorbance at 510 nm was read on an Epoch plate reader (BioTek). Relative growth was determined as (treatment absorbance / control absorbance).
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8

Cultivation and Characterization of Cell Lines

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The breast cancer cell lines included MCF-7 and AMJ13, the human Rhabdomyosarcoma (RD), and the normal beast tissue cell line (HBL) was employed in this study. These cell lines were grown in Dulbecco's Modified Eagle's Medium (DMEM) (Usbiological, USA), which contained 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 g/mL streptomycin (Capricorn- Scientific, Germany). The cell lines were initially maintained as adhesive monolayers growth inside a humidity incubator with 5% CO2 and a temperature of 37°C. After short trypsinization with trypsin-EDTA (Capricorn-Scientific, Germany), cells were collected. These cells are tested and verified on a regular basis [9 (link)].
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9

Metabolic Profiling of MDA-MB-468 Cells

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150.000 MDA-MB-468 cells were plated in 2 ml of DMEM in 6-well plates (VWR #734-0948). After 24 hours of incubation at 37°C, cells were washed with PBS and 2 ml of serine-free DMEM (US Biological Life Sciences #D9802-01), supplemented with 4.5 g/l glucose, 3.7 g/l sodium bicarbonate, 400 μM [2,3,3-2H]-serine, 400 μM glycine, 1:100 glutamax and 10% dialyzed serum, was added for 48 hours. Metabolites for the subsequent mass spectrometry analysis were prepared by quenching the cells in liquid nitrogen followed by a cold two-phase methanol-water-chloroform extraction (20 (link),21 (link)). Phase separation was achieved by centrifugation at 4°C (24x3.75 g, 10 minutes). The methanol-water phase containing polar metabolites was separated and dried using a vacuum concentrator at 4°C overnight. Dried metabolite samples were stored at -80°C. Polar metabolites were analyzed by GC-MS and LC-MS, as described in the supplementary information.
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10

Monocyte Isolation and SAA Stimulation

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We isolated human monocytes using Ficoll-Paque density-gradient centrifugation and EasySep Direct Human Monocyte Isolation Kit (Stemcell Technologies, Grenoble, France). The monocytes were cultured in the presence or absence of SAA (0.01-10 μg/ml; Peprotech, Rocky Hills, NJ, USA) in either amino acid-free (AAF) medium or normal DMEM medium for up to 24 h. The “AAF” culture indicate amino acid-free DMEM (USBiological, Massachusetts) plus 10% FBS.
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