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10 protocols using dmem glutamax supplement

1

Pancreatic Cancer Cell Line Cultures

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In this study, we used a pancreatic ductal adenocarcinoma cell line, PANC-1 (ATCC, Manassas, VA, USA, CRL-1469) (RRID:CVCL_0480), a human pancreatic stellate cell line, RLT-PSC (PSC)[32 (link)] (RRID:CVCL_A5TG), and for control HEK293 cells (ATCC, Manassas, VA, USA, CRL-1573) (RRID:CVCL_0045). Authenticity of cell lines was confirmed using STR profiling and were mycoplasma-free. Cells were grown in high glucose (25 mM) Dulbecco’s modified Eagle’s medium (DMEM GlutaMAX supplement, Thermo Fisher Scientific, Tåstrup, DK, 31,966–047) supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C with 5% CO2. P2X7R function was studied using the specific allosteric inhibitor AZ10606120 (Tocris, Bristol, UK, 3332/10), the competitive inhibitor A438079 (Tocris, Bristol, UK, 2972/10) and the agonist 2′(3′)-O-(4-Benzoylbenzoyl) adenosine 5′-triphosphate triethylammonium salt, BzATP (Sigma, Søborg, DK, 112898-15-4) and ATP (Sigma, Søborg, DK, A9187-1G). Antagonists were dissolved in DMSO (0.1%), agonists were dissolved in physiological buffer and adjusted to pH 7.4.
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2

HaCaT Cell Culture and HPRT Mutation Assay

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Human immortalized keratinocyte-derived (HaCaT) cell line were cultured in a T75 flask, as previously described [119 (link)] using 4500 mg/L Dulbecco’s modified eagle media (DMEM) Glutamax supplement (Thermo Fisher Scientific, Waltham, MA, USA) containing 10% heat-inactivated fetal bovine serum (FBS) and 0.5% antibiotic/antimycotic solution. For HPRT mutation assay, Chinese hamster ovary (CHO) cells were used as described in Section 4.7. Cells were maintained in a humidified incubator at 37 °C with 5% CO2 atmosphere.
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3

Inducible and Constitutive Cas9 Expression in HEK293T Cells

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For pooled experiments, two Cas9-expressing HEK293T cell lines were used. The first expresses Cas9 from a piggybac integrated, TRE3G driven, doxycycline-inducible (1μg/ml) cassette, which we have previously described18 (link). The second expresses Cas9 constitutively from a CBh promoter in the AAVS1 Safe Harbor locus (GeneCopoeia #SL502). All HEK cells were cultured in DMEM +GlutaMax supplement (Thermofisher #10566016).
T25 cultures were transiently transfected with 12.76 ug of pooled plasmid per T25 using Lipofectamine 3000. Cultures were passaged for an additional 48 h. In the inducible Cas9 line, doxycycline was refreshed at passaging. Three days after transfection, cells were collected for sequencing analysis. To prepare samples for sequencing, cell pellets were collected, and gDNA was extracted using a QIAamp DNA mini kit according to the manufacturer’s instructions. DNA was eluted in 200 μl of ultra-pure, nuclease-free water.
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4

Hepatocyte Stress Responses to Metabolic Modulators

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Primary Human Hepatocytes (HH, Lonza, Walkersville, MD, USA) were cultured in Hepatocyte Culture Medium (Lonza) according to the manufacturer’s protocol. HepG2 obtained from ATCC (Sigma-Aldrich, St Louis, MO, USA) were grown in CO2 (5%) incubator at 37 °C in high glucose Dulbecco’s modified Eagle’s medium (DMEM) GlutaMAX Supplement (Thermo Fisher Scientific, San Jose, CA, USA) after addition of 10% (v/v) fetal bovine serum, 100 U penicillin, and 100 μg/mL streptomycin. Human cell lines were tested periodically for mycoplasma by using MycoAlert PLUS detection kit (Lonza). Cells were treated with 500 µM hydroxycitrate (HCA, Sigma-Aldrich) or 200 µg/mL red wine powder (RWP) obtained as previously described from the Italian red wine Aglianico del Vulture [21 (link)]. After 1 h of treatment with HCA or RWP, cells were stimulated with 5 ng/mL of TNFα (Sigma-Aldrich) for up to 24 h. Where indicated, cells were treated also with 20 μM IKK inhibitor VII (IKK 16, Sigma-Aldrich), 5 mM sodium acetate (Ac, Sigma-Aldrich) or 5 mM sodium malate (M, Sigma-Aldrich) alone or in combination with 500 μM NADPH (Sigma-Aldrich).
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5

Cell line characterization for CRC research

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This work was performed in CRC cell lines HCT116 and SW620, which were a kind gift from Prof Ian Tomlinson. This work was also carried out in SW620 ΔCten cell line which was previously established by our group.17 All cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) GlutaMAX ™ supplement (Thermo Fisher Scientific, Carlsbad, CA) antibiotic-free supplemented with 10% foetal bovine serum (FBS) (Sigma, St. Louis, MO) and maintained at 37°C in a 5% CO 2 atmosphere. Cell line identities were authenticated by STR profiling.
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6

Culturing A549 Cells for Experiments

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Human A549 cells (a kind gift from Dr. J. McCauley, MRC NIMR) were maintained in Dulbecco’s modified Eagle’s medium-high glucose, (DMEM GlutaMAX™ Supplement) (gibco-Life technologies) supplemented with 5% fetal calf serum (FCS). A549 cells were seeded on to 24 well plates and when confluent, used for experiments.
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7

Stable Transfection of MN9D Cells

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MN9D-Nurr1Tet-on (iMN9D) cell line stably transfected with pBUD-IRES-eGFP (CTRL cells) or with pBUD-β-globin-MYC IRES-eGFP, 2xFLAG-α-globin (Hb cells) were used [10 (link)]. Cells were maintained in culture at 37 °C in a humidified CO2 incubator with DMEM/F12 medium (Gibco by Life Technologies, DMEM GlutaMAX® Supplement Cat. No. 31966-021; F-12 Nutrient Mix GlutaMAX® Supplement Cat. No. 31765-027) supplemented with 10% foetal bovine serum (Euroclone, Cat. No. ECS0180L), 100 μg/ml penicillin (Sigma–Aldrich), 100 μg/mL streptomycin (Sigma-Aldrich). 300 μg/ml neomycin (Gibco by Life Technologies, Cat. No 11811-031) and 150 μg/mL Zeocin (Invivogen, Cat. No. ant-zn-05) were used for selection.
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8

A549 Cell Culture Protocol

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Human A549 cells (a kind gift from Dr J. McCauley, MRC-NIMR) were maintained in Dulbecco’s modified Eagle’s medium-high glucose, (DMEM GlutaMAX Supplement) (gibco-Life technologies) supplemented with 5% fetal calf serum (FCS). A549 cells were seeded on to 24-well plates and when confluent, used for experiments.
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9

Cell Culture Conditions and Preparation

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Cells were grown at 37 °C and 5% ambient CO2. HeLa Kyoto (ATCC), MDA-MB-231 (ATCC), and A549 cells (ATCC) were grown to ~80% confluence in 140 × 20 mm dishes (NunclonTM Delta Airvent, Thermo Fisher) with Dulbecco’s Modified Eagle’s Medium, high glucose, GlutaMAXTM supplement (DMEM, Thermo Scientific), 10% fetal bovine serum (FBS), and 1% penicillin-streptomycin. H-358 (ATCC CRL-5807) and U-2932 (ATCC) cell lines were cultured in RPMI 1640 with GlutaMAXTM, 1% penicillin-streptomycin, and 10% FBS. Prior to HATRIC-LRC experiments with folate, HeLa cells were starved for 48 h in folate-free RPMI (Gibco).
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10

SILAC Labeling of Polarized Cells

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Cells were grown at 37 °C and 5% ambient CO2 to approximately 80% confluence in 140 × 20 mm dishes (NunclonTM Delta Airvent, Thermo Fisher, Waltham, MA, USA) with Dulbecco’s Modified Eagle’s Medium, high glucose, GlutaMAXTM supplement (DMEM, Thermo Scientific, Waltham, MA, USA), 10% fetal bovine serum (FBS, BioConcept, Allschil, Switzerland), and 1% penicillin–streptomycin. For SILAC labeling, cells were grown in SILAC DMEM high glucose with stable glutamine and without arginine and lysine (Pan Biotech, Aidenbach, Germany), supplemented with 15% dialyzed FBS (Pan Biotech, Aidenbach, Germany), 1% penicillin–streptomycin, 10 mM HEPES (Gibco), non-essential amino acids (Gibco), 200 mg/L L-proline, 42 mg/L L-arginine or L-arginine [10 (link)], and 73 mg/L L-lysine or L-lysine [8 (link)] (Silantes, München, Germany) for 7 days, and the incorporation rate of heavy amino acids was determined to be 95–98% by MS analysis. For polarized cultures, 5 × 106 or 0.5 × 106 cells, respectively, were seeded into 75 mm or 12 mm polycarbonate TranswellsTM with a pore size of 0.4 µm (Corning) and cultured for 6–7 days while changing the medium every second day.
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