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153 protocols using rpmi 1640

1

Evaluation of Monocarbonyl Curcumin Analogs

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All tested monocarbonyl analogs of CUR were dissolved in a cell culture grade DMSO (Sigma Aldrich, Poznan, Poland) followed by ultrasonic mixing for 3 min at rt before use. Immediately after sonication, the appropriate amount of each compound was transferred to a medium to acquire a working concentration of 3000 μg/mL and mixed. The compounds were diluted in X-VIVO 10 (without Phenol red and Gentamycin, Lonza, Koln, Germany) with supplemented with a 10% fetal bovine serum (FBS, PanBiotech) for a 3-(4,5-dimetylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, an RPMI 1640 (PanBiotech, Aidenbach, Germany) for an endotoxin chromogenic assay, or an RPMI1640 supplemented with 10% FBS for a cytokine assay. Working concentrations of all analyzed compounds were prepared using twofold serial dilutions in an appropriate medium to obtain series of 11 dilutions (from 1.46 to 1500 − μg/mL).
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2

Expansion and Culture of Immune Cell Lines

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291PC,13 (link) A20 (ATCC, TIB-208), Phoenix-A (ATCC, CRL-3213), and EBV-LCL were cultured in RPMI 1640 (PAN-Biotech) with 10% FCS, 40 IU/mL penicillin, 40 µg/mL streptomycin, 2 mM l-glutamine, 0.4% vitamin solution, 50 µM β-mercaptoethanol, 1% minimal essential media, and 1 mM sodium pyruvate (all Gibco, Thermo Fisher Scientific). In murine splenocyte culture 50 IU/mL recombinant interleukin (IL)-2 (Proleukin) were added. For in vitro expansion of Marilyn-derived CD4+ splenocytes, cells were activated in anti-CD3 (3 µg/mL; 145–2 C11; Biolegend) and anti-CD28 (2 µg/mL; 37.51; Biolegend) coated plates in the presence of 5 IU/mL IL-2 for 24 hours, harvested and subsequently expanded with addition of 10 IU/mL IL-15 (Biolegend) for 7 days.14 (link) To generate immature dendritic cells monocytes were isolated by adherence and cultured for 5 days in the presence of IL-4 (500 IU/mL; Peprotech), GM-CSF (100 IU/mL; Miltenyi) and TGF-beta (5 ng/mL; Peprotech).
Human T-cells were cultured in RPMI 1640, as mentioned, but with 5% human serum (PAN-Biotech), 5% FCS, and 100 IU/mL IL-2 (Proleukin). Every 11–14 days, T cells were restimulated with 50 Gy irradiated allogeneic feeder cells and 0.8 µg/mL phytohemagglutinin (PHA) (Oxoid), as previously described.15 (link) Culture supernatants of cell lines were regularly tested for mycoplasma contamination (Minerva Biolabs) by PCR.
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3

Breast and Ovarian Adenocarcinoma Cell Lines

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Human breast epithelial adenocarcinoma cell lines (MCF7, MDA-MB-231, MDA-MB-436), and a human ovarian adenocarcinoma cell line (OVCAR-5) were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). Human breast ductal carcinoma cell line; HCC1937 and HCC1937 reconstituted with wild type BRCA1 (HCC1937/wt BRCA1) were kind gifts from Dr. Grant Mc Arthur, Peter MacCallum Cancer Centre, VIC, Australia. All the cell lines were maintained in culture medium containing 10 % Fetal Bovine Serum (FBS) (PAN-Biotech GmBH, Aidenbach, Germany), 0.1 g/L Streptomycin (Sigma Aldrich, St. Louis, MO, USA) and 100U/L Penicillin in a humidified incubator at 37 °C in 5 % (v/v) CO2. MCF7, MDA-MB-231 and OVCAR-5 were maintained in Dulbecco’s Modified Eagles’ Medium (Gibco, Carlsbad, CA, USA), MDA-MB-436 in RPMI 1640 (PAN-Biotech GmBH, Aidenbach, Germany) and HCC1937 and HCC1937/wt BRCA1 in RPMI 1640 with insulin (5 μg/ml). Passage numbers post thawing of the cell lines were noted and experiments were carried out within a maximal passage number (<30).
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4

Culturing Mouse Macrophage and Human Monocyte Cells

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Mouse macrophage cell line, RAW 264.7 (source – ATCC (ATCC® TIB-71™)) was cultured in complete Roswell Park Memorial Institute-1640 medium (RPMI-1640) (PAN Biotech, Aidenbach, Germany) with penicillin (100 U/mL), Streptomycin (0.1 mg/mL), and 2.0 mM L-Glutamine (Himedia Laboratories Pvt. Ltd., Mumbai, MH, India), 10% heat-inactivated fetal bovine serum (FBS) (PAN Biotech, Aidenbach, Germany) at 37ºC in a sterile incubator with 5% CO2 and appropriate humidity. Enzyme-free cell dissociation reagent (ZymeFree™; Himedia Laboratories Pvt. Ltd, Mumbai, MH, India) was used to maintain the cells [56 ].
Undifferentiated human leukemia monocytic cell line, THP-1 (source – ATCC (ATCC® TIB-202™)) was maintained in complete RPMI-1640 (PAN Biotech, Aidenbach, Germany) supplemented with Penicillin (100 U/mL), Streptomycin (0.1 mg/mL), and 2.0 mM L-Glutamine (Himedia Laboratories Pvt. Ltd., Mumbai, MH, India), 10% heat-inactivated FBS (PAN Biotech, Aidenbach, Germany) at 37ºC in a sterile incubator with 5% CO2 and appropriate humidity. THP-1 cells were further treated with 100 ng/ml PMA for 24 h to differentiate monocytes into macrophage-like cells [75 ].
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5

Tumor Cell Dissociation and Isolation

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Tumor tissue was minced and digested with Liberase TM (0.15 Wünsch-Units/ml, Roche) and 10 µg/ml DNaseI (Roche) in FCS-free RPMI-1640 (PAN Biotech) medium with constant mixing (250 rpm), at 37°C for 1 h. Tumor cell suspension was collected through a 100 µm cell strainer into a tube containing RPMI-1640 (PAN Biotech) plus 10% FCS (Biochrom) plus 1% penicillin/streptomycin (Lonza) plus 2 mM glutamine (Lonza) and centrifuged at 300g for 5 min. Red blood cells were lysed by incubation in ACK buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM Na2EDTA) for 2 min at room temperature. Cell suspension was filtered through a 40 µm cell strainer and used for flow cytometry staining.
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6

Epithelial-Mesenchymal Transition in A549 Cells

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The lung adenocarcinoma epithelial cell line, A549, was obtained from the American Type Culture Collection (Manassas, VA, USA) and kindly provided by Prof. Gerhard Hamilton; cells were maintained in RPMI 1640 (PAN™ Biotech) supplemented with 10% fetal bovine serum (FBS, Gibco by Life Technologies) at 37°C, 5% CO2. Cell stimulation was performed in RPMI 1640 (PAN™ Biotech) supplemented with 5% FBS (Gibco by Life Technologies). To trigger the EMT program, cells were seeded in 6-well plates (for RNA isolation and flow cytometry) or in T75 flasks (for lipid extraction) to achieve 40% confluency on the next day and stimulated with TGFbeta at 2 ng/ml (TGF-β1, R&D Systems), TNFalpha at 12.5 ng/ml (human TNF-α, PeproTech) or their combination for 1 h, 2.5 h, 6 h, 24 h, and 48 h. Protocol included a re-stimulation step at 24 h time point. Stimulation conditions for triggering EMT in A549 cells were described previously [28 (link)].
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7

Cell Culture and Metabolic Inhibitors

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HUH7 were obtained from JCRB, BxPC3 and Panc03.27 were obtained from ATCC. STR profiling and routine testing for mycoplasma contamination were performed. HUH7 were grown in DMEM, 10% FCS, BxPC3 were grown in RPMI-1640, 10% FCS and Panc03.27 were grown in RPMI-1640, 15% FCS, 10 Units/ml human recombinant insulin (PAN-Biotech GmbH, Aidenbach, Germany & Sigma-Aldrich). All cells were cultured under constant humidity at 37 °C, 5% CO2. For HUH7, all plastic ware was pre-coated with 0.001% collagen G (PBS). Archazolid A was provided by Rolf Müller, Torin1, CCCP, BPTES, UK5099 and Etomoxir were purchased from Sigma-Aldrich, and dissolved in DMSO (Sigma-Aldrich).
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8

Cell Culture and Lentivirus Infection Protocols

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HeLa, HEK293, MDA-MB-231, MCF-7, and A549 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, high glucose) supplemented with 10% fetal bovine serum (FBS, PAN-Biotech GmbH, Germany). H1975 and BT-549 cells were maintained in RPMI-1640 supplemented with 10% FBS (PAN-Biotech GmbH). Cell lines were routinely tested for mycoplasma contamination detected by PCR (TaKaRa, Japan). Transfection of plasmid/siRNA was performed using Lipo3000® (Thermo Fisher) according to the manufacturer’s instructions. To generate lentivirus for the generation of the indicated stable cell lines, HEK293 cells were plated in 10-cm dishes and transfected with lentiviral plasmids and the lentiviral packaging plasmids pMD2.G and psPAX2 at a ratio of 1:0.5:1. At 48 h after transfection, the supernatant was collected, filtered (0.22 µm filter, Millipore, USA), and later used to infect the indicated cells. At 24 h after infection, cells were further passaged for 1–2 generation and then selected by culture in the presence of puromycin (1 µg/ml) or sorted for green fluorescent protein-positive cells (BD FACSMelody™ Cell Sorter, USA).
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9

Breast Cancer Cell Line Characterization

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Human ER+/HER2-low breast cancer cell lines (MCF-7 [#HTB-22], T47D [#HTB-133], ZR-75-1 [#CRL-1500], and MDA-MB-175 [#HTB-25]) and HEK 293 [#CRL-1573] human embryonic kidney cells were obtained from the American Type Culture Collection. This supplier routinely authenticates cells lines by karyotyping, short tandem repeat profiling, assessment of cell morphology, and species verification by isoenzymology. Upon receipt, cell lines were expanded and aliquots frozen. Cells were passaged for a maximum of 6 months after resuscitation; after 6 months cells were discarded and new aliquots of cells were resuscitated. Cells were cultured in RPMI 1640 or MEM Eagle medium (PAN Biotech GmbH, Aidenbach, Germany) containing 10% fetal calf serum (FCS; PAA Laboratories GmbH, Pasching, Austria) at 37°C in a water-saturated atmosphere containing 5% CO2.
The anti-HER3 antibody lumretuzumab, and the anti-HER2 antibodies pertuzumab (Perjeta®) and trastuzumab (Herceptin®) were obtained from Roche (Penzberg, Germany). The anti-estrogen fulvestrant (Faslodex®) was obtained from AstraZeneca.
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10

Activation of SARS-CoV-2 Spike-Specific T Cells

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Frozen PBMCs were thawed in prewarmed medium (RPMI 1640 [Gibco], 2% FCS [Sigma-Aldrich], and 0.01% Pierce Universal Nuclease [Thermo Fisher Scientific]) on the day of analysis. A total of 200,000 cells (2 × 106/mL) were seeded per well in complete medium (RPMI 1640, 10% heat-inactivated human AB serum [Pan Biotech], and 1% penicillin/streptomycin [Sigma-Aldrich]) in 96-well round-bottom plates (1–4 replicates per stimulation condition, depending on cell counts but to keep conditions within wells constant) and rested for 4 hours at 37°C and 5% CO2. Cells were then stimulated with 1 μg/mL PepMix SARS-CoV-2 spike glycoprotein pool S1 (JPT) and anti-CD28 (Ultra-LEAF purified anti–human CD28 antibody, Biolegend, 302934). For stimulation controls, cells were incubated with DMSO only (unstimulated) or 1 μg/mL staphylococcal enterotoxin B (SEB) (Sigma-Aldrich) only. All conditions were incubated for 16 hours at 37°C and 5% CO2, and Brefeldin A (eBioscience, 00-4506-51) was added after 2 hours.
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