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14 protocols using 35 mm dishes

1

Patch-Clamp Analysis of Cav1.3 Calcium Channels

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The cells were grown on 35 mm dishes (Nunc) to a confluency of about 50%. The cells in each dish were transfected with 4 µg of wild-type rCav1.3 or mutant rCav1.3 R930H cDNA in pCMV6b, 1 µg α2δ1 (Supplementary File: Figure S1) in pCDNA3.1, 1 µg β2b in pCDNA3.1 and 0.2 µg of pEGFP vector using Jetprime (peqlab, Erlangen, Germany), according to the instructions of the manufacturer. After 48 h, CHO cells were recorded in whole cell configuration at room temperature (22 °C) with an EPC-10 amplifier (HEKA). All recordings were digitized at 10 kHz, low-pass filtered at 2 or 5 kHz, analyzed with PulseFIT software (HEKA) and compensated for 60–70% of the series resistance. The pipettes had a tip resistance of 2.5–4.0 MΩ when filled with a solution containing (in mM): Cs-methane sulfonate 120, CaCl2 5, MgCl2 2, EGTA 10, MgATP 2 and HEPES 10 (pH 7.4 CsOH), yielding a [Ca2+i] of about 110 nM (calculated with WinMAxc). The cells were bathed in a solution containing (in mM): NMDG 130, CaCl2 15, KCl 5 and HEPES 10 (pH 7.4, HCl).
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2

Fluorescence Imaging and Beating Rate Analysis

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Fluorescence images and bright-field movies were performed with a Zeiss Axio Observer.Z1 as described above, using a Zeiss LD A-Plan 40×/0.05 Ph2 objective and 35-mm dishes (Nunc) without oil immersion. Movies were taken by Axio Vision LE Modul ‘Digital High Speed Recorder’ with an exposure time of 70 ms per picture, resulting in a 15-s movie with 14 frames per second. To determine the action potential frequency, the beats per minute (bpm) were visually analyzed by four different persons, who simultaneously counted the beating rate in order to determine the average bpm. The average bpm was analyzed from four to six independent transfections and dishes with untransfected HL-1 cells.
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3

Transfection and Patch Clamp of HL-1 Cardiac Cells

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HL‐1 cells were grown in supplemented Claycomb medium at 37°C in an incubator supplied with 5% CO2 as previously described (Claycomb et al, 1998). Cells were split in a 1:3 ratio when they were 100% confluent and had the ability to beat. For transfection, HL‐1 cells were seeded on 35‐mm dishes (Nunc) previously coated with gelatin/fibronectin in a 1:2 ratio; 24 h after seeding, cells were transfected with either 1.5 μg of TREK‐1‐EGFP or TREK‐1I267T‐EGFP cDNA constructs using Lipofectamine 2000 (Invitrogen) following manufacturer instructions. After 24 h, transfection media was exchanged and cells were incubated for 4 h in supplemented Claycomb media. Subsequently, the 100% confluent and beating cells were used in patch clamp and imaging experiments.
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4

Murine Hematopoietic Stem Cell Assay

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One milliliter of colony assay medium (MethoCult GF M3434, Stem Cell Technologies) contained 1 × 104 GFP+ cells, which were sorted from mouse BM cells infected with lentiviruses. The cells were plated in 35-mm dishes (Nunc). Each sample was plated in triplicate. Colony counts were scored, and re-platings occurred every 7 d.
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5

Intracellular ROS Measurement by DCFH-DA Assay

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The intracellular ROS level was determined by 2′7′-dichlorofluorescin diacetate (DCFH-DA) assay. Briefly, the PAM212 cells were seeded in 35 mm dishes (Nunc, Denmark) and incubated with BA or NAC for 24h before UVB irradiation. After 100 mJ/cm2 UVB exposure, the cells were washed three times with PBS and then incubated with culture medium containing 10 μM DCFH-DA (Sigma, Sigma-Aldrich Co, U.S.A) for 30 min at 37°C in the dark. Thereafter, the cells were washed with PBS three times and collected for observation and flow cytometry detection. The ROS-positive cells were visualized and counted using fluorescence microscopy with excitation at 485 nm and emission at 538 nm. For flow cytometry detection, the cells were analyzed with a FACS flow cytometer.
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6

Cortical Neuron Culture and Hedgehog Signaling

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Cultures of pure cortical neurons were obtained from mice at embryonic day 14.5. In brief, cortices were isolated and treated with 0.125% trypsin + EDTA (Life Technologies) for 5 min at 37 °C. trypsin was inactivated with DMEM/F12 + 10% FBS. Cells were then dissociated by gentle pipetting in Neurobasal medium (Life Technologies) supplemented with 0.5% Glutamax (Life Technologies), 1% Penicillin/Streptomicin, and 2% B27 supplement, and 600,000 cells/well were plated in 35 mm dishes (Nalge Nunc International, Rochester, NY) precoated with 0.1% gelatin (Sigma-Aldrich) and 50 μg/ml poly-L-lysine (Sigma-Aldrich). After 5-days in vitro, neurons were treated with 5 μM 20 S for 5 or 30 min. 10T1/2 cells were cultured and used as positive controls for Gli-1 expression (see supplementary methods).
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7

NLS-HK2 Transduction and Colony Counting

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NB4 cells transduced with NLS1–HK2 or NLS2–HK2 were plated in duplicate 35-mm dishes (Nunclon) to a final volume of 1 ml per dish in MethoCult H4100 medium (StemCell Technologies) supplemented with 30% FBS. After incubation for 7–8 d at 37 °C and 5% CO2 with 95% humidity, the number of colonies containing ten or more cells was counted on an inverted microscope. The plating efficiency was determined by counting the number of colonies that formed: (number of colonies formed ÷ number of cells inoculated) × 100.
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8

Hematopoietic Colony Forming Assay

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The cultured CD34+ cells from all experimental and control groups were separated and centrifuged at 300×g for 5 min. One thousand cells were then seeded into 35-mm dishes (Nalge Nunc International) containing 0.5 ml of semisolid methylcellulose in Methocult H4435 medium (StemCell Technologies). The 35-mm dishes were incubated at 37 °C in a 5% CO2 in air atmosphere for 14 days. Burst forming unit-erythroid (BFU-E), colony-forming unit-granulocyte-erythrocyte-monocyte-megakaryocyte (CFU-GEMM), and colony-forming unit-granulocyte-macrophage (CFU-GM) colonies that were formed after 14 days were counted and classified based on morphology as described by the Atlas of Hematopoietic Colonies from Cord Blood. The CFU colonies were photographed using an inverted phase-contrast microscope (Nikon Instruments, Tokyo, Japan). CFU numbers were then calculated by dividing the number of colonies at day 14 by the number of cells plated and multiplying this value by 10,000 which reflected the colony-forming ability of 10,000 cells.
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9

MTT Assay for Radiation Cytotoxicity

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The cells were collected in 35-mm dishes (Nunc), irradiated with 0.5, 1, 10 or 30 Gy after 2 d, and incubated for 6–48 h. We confirmed the presence of formazan crystals after 2 h of incubation with the MTT solution (0.1 mg/dish; Sigma). The formazan crystals in each dish were dissolved in 700 µl DMSO (Sigma) and transferred to 96-well plates (200 µl in each of three wells). Spectrophotometry was performed at 540 nm using an iEMS Reader MF (Labsystems, USA).
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10

Culturing Immortalized Human Corneal Epithelial Cells

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The immortalized human corneal epithelial cell line (HCEC) has been previously described.29 (link),30 (link),37 (link) While standard short-tandem repeat (STR)-based validation of this line is not possible due to lack of availability of the original source cells, we do routinely check the cells for the presence of keratin K12 and keratin K3 mRNA by PCR. All cells were grown in Dulbecco's modified Eagle's medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with fetal bovine serum (3%), 1% insulin-transferrin-selinium (ITS; BD Biosciences, Bedford, MA, USA), and 40 μg/mL gentamicin (Life Technologies, Grand Island, NY, USA). Cells were subpassaged using trypsin (Sigma, Ann Arbor, MI, USA) digestion, seeded in 35-mm dishes (Fisher Scientific, Breinigsville, PA, USA), and cultured in a humidified incubator at 37°C with 5% CO2. Culture medium was replaced every 2 days. HCEC and all cultured cells in this study were found to be mycoplasma negative (Mycoplasma Detection Kit; R&D Systems Inc, Minneapolis, MN, USA)
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