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76 protocols using p4333

1

Culturing Human Cell Lines for Research

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The human colon adenocarcinoma cell line Caco-2 (86010202, Sigma, St. Louis, MO, United States) was cultured in Eagle’s minimum essential medium (EMEM; 30-2003, ATCC, Manassas, VI, United States)) supplemented with 10% fetal bovine serum (FBS; 16140-071, Gibco, Gaithersburg, MD, United States), 1% non-essential amino acids (NEAA; 11140-050, Life Tech, Carlsbad, CA, United States), and 1% penicillin/streptomycin (P4333, Sigma). The human colon cell line HT29-MTX-E16 (86010202, Sigma) was cultured in Dulbecco’s modified Eagle’s medium (DMEM; D6546, Sigma) supplemented with 10% FBS (16140-071, Gibco), 1% NEAA (11140-050, Life Tech), 1% Glutamax (35050-061, Gibco), and 1% penicillin/streptomycin (P4333, Sigma). The human acute monocytic leukemia cell line THP-1 (Tib-202, ATCC) was cultured in Roswell Park Memorial Institute (RPMI) 1640 (R0883, Sigma) supplemented with 10% FBS (16140-071, Gibco), 1% Glutamax (35050-061, Gibco), and 1% penicillin/streptomycin (P4333, Sigma). The cells were tested for mycoplasma contamination and found negative.
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2

Expansion of Human Bone Marrow Mesenchymal Stem Cells

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Four healthy donors of human bone marrow-derived mesenchymal stem cells (hBM-MSCs) were purchased from Rooster Bio (MSC-003 lots: 00182, 310,271, 310,267 and 310,263) and used in the experiments with population doubling levels (PDL) between 13.2 and 15. The donors were derived from two females and two males, with ages ranging from 19 to 26 years. Cells were expanded in DMEM high glucose (D6429, Sigma) supplemented with 10% heat-inactivated fetal bovine serum (F4135, Sigma) and 1% penicillin–streptomycin (P4333, Sigma) and maintained at 37℃ and 5% CO2 in a humidified incubator. Peripheral blood mononuclear cells (PBMCs) were purchased from Cell Applications, Inc. (690 PB-100a) and maintained in RPMI-1640 medium (R8758, Sigma) supplemented with 10% heat-inactivated fetal bovine serum (F4135, Sigma), 1% penicillin–streptomycin (P4333, Sigma-Aldrich) and 1% nonessential amino acids—NEAA (M7145, Sigma).
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3

Standardized Fibroblast Culture for Seahorse Analysis

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PD patients’ fibroblasts were prepared isolated at Leiden University Medical Center from skin biopsies derived from the ventral side of the upper leg and cultured under highly standardized conditions at 37°C and 5% Carbon dioxide (CO2) up to a maximum of 10 passages. The number of passages was kept consistent within groups. Fibroblasts were maintained in Dulbecco's Modified Eagle Medium (DMEM) 10% Fetal Bovine Serum (FBS) and 1% penicillinstreptomycin (P4333, Sigma‐Aldrich) until reaching confluency. Prior to Seahorse analysis, fibroblasts were rinsed with Phosphate‐Buffered Saline (PBS) and cultured with glucose (glucose 10 mM, 10% FBS [F6178, Sigma‐Aldrich], 2 mM glutamine, 5 mM Hepes, and 1% penicillinstreptomycin (P4333, Sigma‐Aldrich, St. Louis, MI, USA) or galactose (galactose 10 mM, 10% FBS, 2 mM glutamine, 5 mM Hepes, and 1% penicillinstreptomycin) medium for 3 days. Fibroblasts from sex‐matched controls of comparable age were either obtained from the Coriell biorepository (identification codes AG04659, AG05266, AG06283, AG07936, AG08152, AG08268, AG08269, AG08543, AG09162, AG09271, AG09879, AG12428, AG12951, AG13077, AG13348), Coriell Institute for Medical Research (Camden, New Jersey), or from the biorepository available in the Department of Molecular Genetics of the Erasmus Medical Center (MC), Rotterdam, The Netherlands.
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4

Culturing Human Neuroblastoma and Rat Pheochromocytoma Cells

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Human neuroblastoma SH-SY5Y cells (ATCC) were grown in Dulbecco’s modified Eagle’s medium (DMEM, #11995073, GIBCO) with 10% fetal bovine serum (FBS, vol/vol, #26140079, GIBCO) and a penicillin–streptomycin antibiotic solution (100 U/mL, #P4333, Sigma-Aldrich). PC12 cells, noradrenergic clonal cells obtained from the adrenal medulla of Rattus norvegicus (ATCC), were grown in DMEM (#11995073, GIBCO) containing 10% FBS (vol/vol, #26140079, GIBCO), 5% Horse serum (vol/vol, #26050-088, GIBCO), 2 mM Glutamine (#G7513, Sigma-Aldrich), and penicillin–streptomycin antibiotic solution (100 U/mL, #P4333, Sigma-Aldrich). Both types of cells were grown at 37°C in a humidified atmosphere consisting of 5% CO2/95% air. X-tremeGENE HP transfection reagents (#6366546001, Roche) were used for transient transfection, following the manufacturer’s instructions.
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5

Mesenchymal Stem Cell and Macrophage Differentiation

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For cell culture experiments, we used mesenchymal stem cells (hMSC): bone marrow-derived (female, 26 years) and adipose-derived (female, 18-30 years) and THP-1 cells, purchased from RoosterBio and American Type Culture Collection (ATCC), respectively. The hMSC cells were maintained in DMEM high glucose medium with L-glutamine (D5796, Sigma-Aldrich), supplemented with 10% heat-inactivated fetal bovine serum (FBS) (F6765, Sigma-Aldrich), 1% penicillin–streptomycin (P4333, Sigma-Aldrich), and 1% NEAA (M7145, Sigma Aldrich). The THP-1 cells were maintained in RPMI-1640 medium (R7388, Sigma-Aldrich), supplemented with 10% heat-inactivated fetal bovine serum (FBS) (F6765, Sigma-Aldrich), 1% penicillin–streptomycin (P4333, Sigma-Aldrich), and 0.05 mM 2-mercaptoethanol. All cells were cultured at 37 °C in 5% CO2 and were mycoplasma-free. The hMSC passages were performed at 75-80% confluence using 0.25% trypsin (59418C, Sigma-Aldrich). The hMSCs were used below seven passages, and the THP-1 cells were used below 40 passages. Viable cells were counted using a hemocytometer and the trypan blue exclusion method (T8154, Sigma–Aldrich). The differentiation of THP-1 monocytes to macrophages occurred after treatment with 18 nM of phorbol 12-myristate 13-acetate (1585, Sigma-Aldrich) for 12 hrs. Macrophage M2 polarization was performed using 20 ng/mL of IL-13 and 20 ng/mL of IL-4 for 72 hrs.
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6

Mesenchymal Stem Cell and Macrophage Differentiation

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For cell culture experiments, we used mesenchymal stem cells (hMSC): bone marrow-derived (female, 26 years) and adipose-derived (female, 18-30 years) and THP-1 cells, purchased from RoosterBio and American Type Culture Collection (ATCC), respectively. The hMSC cells were maintained in DMEM high glucose medium with L-glutamine (D5796, Sigma-Aldrich), supplemented with 10% heat-inactivated fetal bovine serum (FBS) (F6765, Sigma-Aldrich), 1% penicillin–streptomycin (P4333, Sigma-Aldrich), and 1% NEAA (M7145, Sigma Aldrich). The THP-1 cells were maintained in RPMI-1640 medium (R7388, Sigma-Aldrich), supplemented with 10% heat-inactivated fetal bovine serum (FBS) (F6765, Sigma-Aldrich), 1% penicillin–streptomycin (P4333, Sigma-Aldrich), and 0.05 mM 2-mercaptoethanol. All cells were cultured at 37 °C in 5% CO2 and were mycoplasma-free. The hMSC passages were performed at 75-80% confluence using 0.25% trypsin (59418C, Sigma-Aldrich). The hMSCs were used below seven passages, and the THP-1 cells were used below 40 passages. Viable cells were counted using a hemocytometer and the trypan blue exclusion method (T8154, Sigma–Aldrich). The differentiation of THP-1 monocytes to macrophages occurred after treatment with 18 nM of phorbol 12-myristate 13-acetate (1585, Sigma-Aldrich) for 12 hrs. Macrophage M2 polarization was performed using 20 ng/mL of IL-13 and 20 ng/mL of IL-4 for 72 hrs.
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7

Culturing ER+ Breast Cancer Cell Lines

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MCF-7 and T-47D, two human ER (+) breast carcinoma cell lines were used for this study. Both cell lines were purchased from American Type Culture Collection (ATCC). MCF-7 cells were maintained in DMEM high glucose media with l-Glutamine (D5796, Sigma-Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (FBS; F6765, Sigma-Aldrich) and 1% penicillin/streptomycin (P4333, Sigma-Aldrich). T-47D cells were maintained in RPMI medium 1640 with l-Glutamine (11875–093, ThermoFisher Scientific) supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin. RPMI and DMEM high glucose media without l-Glutamine, sodium pyruvate and phenol red (D1145, Sigma-Aldrich) supplemented with 10% FBS charcoal-stripped (F6765, Sigma-Aldrich) and 1% penicillin/streptomycin (P4333, Sigma-Aldrich) were used for the experimental conditions of MCF-7 and T-47D cells. All cells were cultured at 37 °C in a 5% CO2 humidified environment. Cultures were periodically verified and confirmed to be free of mycoplasma. Passages were performed at 75–80% confluence using 0.5% trypsin (59418C, Sigma-Aldrich). Cell lines were used below 20 passages. Viable cells were identified using the Trypan Blue (T8154, Sigma-Aldrich) exclusion method and counted using a hemocytometer.
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8

Establishment of Neuroblastoma Primary Cultures

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30 samples derived from 24 patients with neuroblastoma were included in this study. All tumor samples were collected from patients at the Great Ormond Street Hospital following written informed consent. In the case of minors, consent was obtained from adults with parental responsibility, with written assent from the child being optional for older participants. Ethical approval for the study was obtained through the national United Kingdom research ethics application system of the UK Health Research Authority; reference 14/WM/1253 “Establishing primary cultures and cell lines from pediatric cancers”. Tumor tissue was disaggregated manually into 1–2 mm fragments in X-VIVO 15 media (BE02-060F, Lonza) supplemented with 5% heat-inactivated human AB serum (H3667, Sigma-Aldrich), 100IU/mL penicillin (P4333, Sigma-Aldrich) and 100 μg/mL streptomycin (P4333, Sigma-Aldrich).
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9

Culturing Human Airway Epithelial Cells

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BEAS-2B cells were purchased from American Type Culture Collection (ATCC® CRL-9609TM, In Vitro Technologies, Melbourne, Victoria, Australia) were cultured in BEGMTM bronchial epithelial cell growth medium BulletKitTM (CC3170, Lonza, Mount Waverley, Victoria, Australia) containing BEGMTM basal medium (CC-3171, Lonza, Mount Waverley, Victoria, Australia) and BEGMTM SingleQuotsTM supplements (CC-4175, Lonza, Mount Waverley, Victoria, Australia) supplemented with 1% penicillin/streptomycin (P4333, Sigma, North Ryde BC, New South Wales, Australia) and 1% amphotericin B (A2942, Sigma, North Ryde BC, New South Wales, Australia). Human small airway epithelial cells (SAECs) (CC-2547, purchased from Lonza, Mount Waverley, Victoria, Australia) were cultured in SAGMTM small airway epithelial cell growth medium BulletKit (CC-3118, Lonza, Mount Waverley, Victoria, Australia) containing SABMTM basal medium (CC-3119, Lonza, Mount Waverley, Victoria, Australia) and SAGM SingleQuotsTM supplements (CC-4124, Lonza, Mount Waverley, Victoria, Australia) supplemented with 1% penicillin/streptomycin (P4333, Sigma, North Ryde BC, New South Wales, Australia) and 1% amphotericin B (A2942, Sigma, North Ryde BC, Australia), grown in flasks coated in bovine collagen I (A10644-01, Life Technologies, Scoresby, Victoria, Australia). Cells were maintained in a humidified incubator (37 °C, 5% CO2).
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10

Cell Culture and BH3 Mimetics Protocol

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U87 glioblastoma cells were purchased from the ATCC (Manassas, Virginia, USA) and cultivated in Dulbecco's modified Eagle's high glucose medium (DMEM, D5796, Merck, Darmstadt, Germany) supplemented with 10% FBS (D7524, Merck), 1% non-essential amino acids and 1% antibiotics (penicillinstreptomycin, P4333, Merck). Mantle cell lymphoma (MCL) cell line HBL-2 was obtained from Prof. Pavel Klener (HBL-2 cells were originally obtained from Prof. Martin Dreyling, Munich, Germany), and cultivated in Iscove's Modified Dulbecco's Medium media (IMDM, I7633, Merck) supplemented with 15% FBS (F7524, Merck) and 1% antibiotics (Penicillin-Streptomycin, P4333, Merck). Cultured cells were regularly tested for mycoplasma infection using the MycoAlert™ kit (LT07-318, Lonza, Basel, Switzerland), and only mycoplasma-negative cells were used. BH3 mimetics were purchased from MedChemExpress (Monmouth Junction, New Jersey, USA) and, unless stated otherwise, all other chemicals were from Merck. HCT-116 Bax/Bak -/-cells were kindly provided by Richard Youle (National Institutes of Health, Bethesda, Maryland, USA).
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