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10 protocols using amphotericin

1

Cell Line Cultivation for Breast Cancer Research

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MDA-MB-231 cells were obtained from American Tissue Culture Collection. Cancer associated fibroblasts were isolated from invasive breast ductal carcinoma and characterized in previous studies [95 (link), 96 (link)]. DCIS.com cells were generously provided by Fariba Behbod, PharmD, Ph.D (University of Kansas Medical Center). Raw 264.7 mcherry cells were generously provided by George Veilhauer, Ph.D (University of Kansas Medical Center, Kansas City, KS). All cell lines were cultured on plastic in DMEM media containing 10% FBS with 0.1% amphotericin, 1% penicillin-streptomycin (cat no. 30-004-CI, Cellgro).
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2

Murine and Human Cancer-Associated Fibroblasts

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Murine fibroblast lines (41CAF, 83CAF, 311NAF) were isolated and characterized in previous studies [20 (link), 27 (link), 28 (link)]. Briefly, 41CAFs and 83CAFs were isolated from transgenic mice (FVB) expressing the PyVmT oncogene under the control of the Mouse Mammary Tumor Virus Promoter (MMTV), at 12–16 weeks of age. Normal mammary fibroblasts (311NAF) were isolated from the mammary glands of wild-type C57BL/6 mice at 12–16 weeks of age. Human cancer associated fibroblasts were isolated from patient specimens of invasive breast ductal carcinoma, using methods previously described [27 (link)]. 4T1 mammary carcinoma cells were generously provided by Fred Miller (University of Michigan, Ann Arbor, MI). All cell lines were cultured on plastic in DMEM media containing 10% FBS with 0.1% amphotericin, 1% penicillin-streptomycin (Cellgro).
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3

ARPE-19 Cell Culture Conditions

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The ARPE-19 cells are available from the American Type Culture Collection (ATCC) (Manassas, Virginia, USA). They are cultured under standard conditions (37°C in a humidified chamber of 5% CO2 in Dulbecco's modified Eagle's medium: nutrient mixture F-12 (DMEM/F-12) (Thermo Scientific, Wyman, Massachusetts) supplemented with 10% fetal bovine serum, 10,000 U/mL penicillin, 10 mg/mL streptomycin sulfate, and 25 μg/mL amphotericin (Cellgro, Manassas, Virginia) which was changed every 3 days. Cells were passaged weekly at a ratio of 1 : 10.
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4

Isolation and Stimulation of PBMCs

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Blood was vested in heparin tubes. PBMCs from healthy human volunteers were isolated by Histopaque-1077 (Sigma-Aldrich, Germany) gradient centrifugation. The cells from the interPHAse were harvested, washed in 0.9% NaCl (Kabe, Germany), and suspended at a density of 1 × 106 cells/ml in RPMI supplemented with 10% heat-inactivated fetal calf serum (Sigma-Aldrich) 2 mM glutamine (Sigma-Aldrich, Germany), Antibiotic-Antimycotic solution 100 I.U. penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin (Corning, BD, USA). Cells were divided into 2 groups with or without addition of 400 ng/ml SC (Sigma-Aldrich) and cultured in 24-well plates (Nunc, Thermo Fisher, USA), then incubated for 48 hours at 37°C in 5% CO2 atmosphere. Initially, research was performed on cells stimulated for 4 hours by incubation with 50 ng/ml PMA (Sigma-Aldrich), 1 μg/ml ionomycin (Sigma-Aldrich), and 4 μl/ml Golgi-Stop (Becton Dickinson (BD), USA). Subsequently, we determined cytokine production in cells stimulated with 2 μg/ml PHA (Sigma-Aldrich) for 12 hours in the presence of 4 μl Golgi-Stop (Becton Dickinson, USA) per 1 ml of culture.
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5

Isolation of Chicken Embryonic Cells

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Thirty fertilized eggs of Single Comb White Leghorn chickens were purchased from a local hatchery (Koiwai Farm Co., Ltd, Shizukuishi, Iwate, Japan). Embryonic cells from various tissues were prepared as described previously (Kita and Makino, 2014 ). Briefly, fertilized eggs were incubated for 19 days, and embryos were taken from eggs. After decapitated, breast muscles, liver, spleen and kidney were removed and minced finely with scissors. Minced tissues were gently digested using 0.25% (w/v) trypsin, pipetted several times and passed though the gauze to remove the crumble of tissues. Cells were seeded in a Type-1 collagen-coated 48-well plate (Corning, Bedford, MA, USA) with Medium 199 including 2.5 µg/ml amphotericin, 100 units-100 µg/ml penicillin-streptomycin, 50 µg/ml gentamycin and 10% fetal calf serum (FCS) and incubated at 37°C in 5% CO2/95% air (v/v). All reagents except penicillin-streptomycin for preparation of various tissue cells were purchased from Thermo Fisher Scientific (Waltham, Massachusetts, USA). Penicillinstreptomycin was purchased from Biological Industries Ltd. (Kibbutz Beit Haemek, Israel).
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6

Porcine Earlobe Fibroblast Isolation

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Bovine earlobe fibroblasts have been previously reported [19 (link)]. Pieces of swine earlobes were obtained from the Rakuno Gakuen Field Education Center
(Ebetsu, Japan) when pigs (aged 3 days) were ear-notched. The swine earlobe tissue blocks were cut into fragments, and vigorously washed with phosphate-buffered saline (PBS) containing 200
U/ml penicillin, 200 µg/ml streptomycin, and 500 ng/ml amphotericin B (Nacalai Tesque, Kyoto, Japan).
Subsequently, the tissues were treated with 2 mg/ml collagenase type I (Wako Pure Chemical, Osaka, Japan) in Tyrode’s solution and cut into small pieces using scissors. The
tissue slices were further digested for 30 min at 37°C with strong agitation. After extensive washing with PBS and centrifugation, the pellet was resuspended in Dulbecco’s modified Eagle
medium (DMEM) containing 10% fetal calf serum (FCS), 200 U/ml penicillin, 200 µg/ml streptomycin, and 500
ng/ml amphotericin, and filtrated with a cell strainer (70 µm; Corning, New York, NY, USA) to remove debris. The cells were cultured in
DMEM supplemented with 10% FCS at 37°C, 5% carbon dioxide, and 95% humidity.
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7

Overexpression of USP20 in Cancer Cells

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HEK293T, MDA-MB-231, LM2, and SCP28 cell lines were maintained in DMEM medium (Sigma) supplemented with fetal bovine serum (10%; Gemini Bio Products), penicillin/streptomycin (1%; Corning), and amphotericin (0.2%; Corning). SUM159-M1a cells were grown in F12 medium supplemented with 10% FBS, 10 μg/mL insulin, and 20 ng/mL EGF. Plasmids or siRNAs were transfected into cells using Lipofectamine 2000 or RNAiMax following the manufacturer's manual (Life Technology).
To generate lentiviruses for USP20 overexpression, pLEX empty vector, pLEX-USP20, or pLEX-USP20-C154S was cotransfected with VSV-G and p8.9 into HEK293T cells. Media containing viruses were collected 2 and 3 d after transfection. Recipient LM2 cells were incubated with virus-containing media supplemented with 2 μg/mL polybrene for 24 h. To generate stable cell lines, puromycin was used to select the infected cells.
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8

Authenticated Cell Lines Transfection Protocol

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MDA-MB-231 and MCF7 cell lines(authenticated by STR profiling and tested for mycoplasma contamination) were cultured in DMEM (Gibco) supplemented with foetal bovine serum (10%; NEWZERUM), penicillin/streptomycin (1%; Corning), and amphotericin (0.2%; Corning). Plasmids or siRNAs were transfected using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions. To generate stable cell lines, puromycin was used to select the infected cells.
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9

Cell Line Culture and Authentication

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SW480, LS174T, and CT26 cell lines were obtained from ATCC. HEK-293LTV cells were obtained from Cell Biolabs. LS174T, HEK-293LTV, and CT26 cells were grown in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% v/v fetal bovine serum (Corning), L-glutamine (2 mM; Gibco), penicillin-streptomycin (100 U/ml; Gibco), Amphotericin (1 μg/ml; Lonza), and sodium pyruvate (1 mM; Gibco). SW480 cells were grown in McCoy’s 5A modified media with L-glutamine (Corning) supplemented with 10% v/v fetal bovine serum, penicillin-streptomycin (100 U/ml), Amphotericin (1 μg/ml), and sodium pyruvate (1 mM). All cells were grown at 37°C under 5% CO2 and passaged when the monolayer reached 80% confluency. All cell lines were authenticated by SPR profiling at MSKCC. All cells were regularly checked for mycoplasma contamination and have been negative.
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10

PBMC Isolation from Whole Blood

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Blood was vested in heparin tubes. PBMCs were isolated by gradient centrifugation, 800× g, 12 min on Histopaque-1077 (MERCK, Darmstadt, Germany). The cells from the interphase were harvested and washed in phosphate-buffered saline (PBS) (Aqua-Med, Łódź, Poland) 600× g, 10 min. This step was repeated twice. Then cells were resuspended in RPMI enriched with 10% heat-inactivated fetal calf serum (MERCK, Darmstadt, Germany), 2 mM glutamine (MERCK, Darmstadt, Germany), antibiotic-antimycotic solution 100 I.U., penicillin, 100 µg/mL Streptomycin, and 0.25 µg/mL Amphotericin (Corning, New York, BD, USA).
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