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48 protocols using d6046

1

Culturing HEK293 Cell Lines

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Human embryonic kidney 293 Freestyle (HEK293F) cells were maintained in Expi293 Expression Medium (Gibco, Waltham, MA, USA), at 37 °C in an 8% CO2 atmosphere. Human embryonic kidney (293T) cells were maintained in the Dulbecco’s Modified Eagle Medium (D6046, Merck, Darmstadt, Germany) supplemented with 10% fetal bovine serum (FB-1365, Biosera, France).
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Culturing Human Retinal Vascular Endothelial Cells

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The HRVECs were obtained from Otwo Biotech (Shanghai, China) and cultured at 37°C with 5% CO2. Cells were maintained in Dulbecco's modified Eagle's medium (D6046; Merck, Darmstadt, Germany) containing 10% fetal bovine serum (SH30406.05: Hyclone, Logan, UT, USA) and 1% penicillin/streptomycin (SV30010-5; Hyclone). The HRVECs from passages 3–7 were used for further experiments.
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3

Microbial Growth Conditions Optimization

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E. coli strains were grown in Luria-Bertani broth (LB). S. aureus strains were grown in tryptic soy broth (TSB; Becton, Dickinson); Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco 22400089); low-glucose Dulbecco’s Modified Eagle’s Medium (DMEM; Merck D6046) supplemented with 2 mM l-glutamine and 10% FBS; or human serum from male AB plasma (Merck H4522) at 37°C.
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4

Autophagy Regulation in Cell Lines

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We used human HeLa cells (ATCC CCL-2), MEFs, Atg5 KO MEFs (Kuma et al., 2004 (link)), and CRISPR-Cas9–generated HeLa ATG7 KO cells (Mejlvang et al., 2018 (link)). All cells were cultured in DMEM (D6046; Sigma-Aldrich) supplemented with 10% FBS (S0615; Biochrom) and 1% streptomycin-penicillin (P4333; Sigma-Aldrich) and kept in a humidified incubator at 37°C and 5% CO2. Starvation experiments were conducted by incubating cells in HBSS (H9269; Sigma-Aldrich). Cells were treated with 1 µg/ml tetracycline (Sigma-Aldrich), 200 ng/ml BafA1 (sc-201550; Santa Cruz Biotechnology), and 25 µM MG132 for the indicated time periods. DNA transfection was done with Metafectene Pro (T040; Biontex) according to the manufacturer’s protocol. siRNA transfections were done with RNAiMAX according to the manufacturer’s protocol.
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5

Cell Culture Protocols for Tumor Cell Lines

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CMT 167 cells (kind gift from Prof. Paola Allavena, Humanitas Research Hospital) were cultured in Gibco Dulbecco's Modified Eagle Medium (DMEM), high glucose (Sigma‐Aldrich, #D5796), with 10% Fetal Bovine Serum (FBS, Sigma‐Aldrich #F7524), 2 mM L‐glutamine and 100 U/mL penicillin–streptomycin (Pen/strep). 4T1 cells (CRL‐2539, American Type Culture Collection (ATCC)) were grown in RPMI 1640 Medium with 10% FBS and 100 U/mL Pen/strep. KPCY cells (2838c3, Kerafast) were cultured in DMEM (Sigma‐Aldrich #D5796) with 10% FBS and 100 U/mL Pen/strep. MC38 cells (ENH204, Kerafast) were cultured in low glucose DMEM (Sigma‐Aldrich #D6046) with 10% FBS, 2 mM L‐ glutamine, 1* non‐essential amino acids, 1 mM sodium pyruvate, 10 mM HEPES (4‐(2‐hydroxyethyl)‐1‐piperazineethanesulfonic acid), and 100 U/mL Pen/strep. All chemicals were from Sigma‐Aldrich unless specified. Cells were thawed and maintained in exponential growth for 2–3 weeks at 37°C and 5% CO2 before implantation.
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6

Establishing Primary Human Fibroblast Cultures

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Primary patient fibroblasts were grown from skin biopsy specimen and the immortalized line was generated by stable expression of hTERT. The human normal fibroblast lines were obtained from ATCC. The fibroblasts were maintained in low-glucose DMEM (Sigma, D6046) supplemented with 5% heat-inactivated fetal bovine serum (FBS), and cultured at 37°C with 5% CO2.
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7

Overexpression and Characterization of Piezo1 in HEK293T Cells

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Human embryonic kidney cells (HEK 293T/17, ATCC-LGC Standards, Manassas, Virginia, USA) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with low glucose (D6046, Sigma-Aldrich, Hamburg, Germany) supplemented with 10% fetal calf serum (F9665, Sigma-Aldrich, Hamburg, Germany) and 1% penicillin/streptomycin (P4333, Sigma-Aldrich, Hamburg, Germany). HEK cells offer the advantage of being easy to transfect even with large constructs and thus represent a widely used cell culture model for overexpression experiments. We use HEK cells to overexpress the 2521 amino acid protein Piezo1 (Uniprot entry Q92508, Section 2.1.2) and to test the effects of various compounds on Piezo1-induced cell stiffening (Section 2.1.3).
A human atrial fibroblast line (HAF, [36 (link)]) was cultured in DMEM supplemented with 2 mM L-alanyl-L-glutamine (GlutaMAX, 31966021, LifeTechnologies, Darmstadt, Germany), 10% fetal calf serum and 1% penicillin/streptomycin. At ≈90% confluence, cells were detached using Trypsin-ethylene-diamine-tetraacetic acid (59418C, Sigma-Aldrich, Hamburg, Germany) and seeded in fresh polystyrene flasks (Z707538, TPP, Trasadingen, Switzerland) for maintenance, or on various substrates for experiments (see below).
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8

Establishment of HeLa Cell Lines Expressing ELP Fusion Proteins

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We cultured HeLa cells in Dulbecco’s modified Eagle medium (DMEM; D6046, Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS; Biowest) at 37 °C in a 5% CO2 incubator. We seeded cells on in-house-made glass bottom dishes and grew up to 60–70% of cell confluence before performing transfection. For transfection, we mixed 2.0 µg of plasmids and 5.0 µg of polyethylenimine MAX (24765–1, Polysciences) in 200 µL of Opti-MEM medium (31985-070, Thermo Fisher Scientific), and incubated for 20 min at room temperature. Subsequently, we added the mixture to 1 mL of culture medium containing HeLa cells, and exchanged the culture medium at 6 h after the mixing. We cultured the cells for ~ 48 h and exchanged the medium to DMEM/F12 (11039-021, ThermoFisher Scientific) without phenol red before microscopy observation.
To establish a HeLa cell line stably expressing ELP-TEMP or ELP-REF, 2 days after transfection, we exchanged the culture medium with DMEM supplemented with 10% FBS and 500 µg/mL geneticin (G-418, 10131-035, Gibco). We kept culturing the cells until colonies formed. Finally, we isolated a fluorescent colony and grew up in the same medium to increase the cell number. After establishing the stable cell lines, we grew them with a DMEM medium containing 10% FBS and 200 µg/mL geneticin.
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9

Cell Migration and Invasion Assay

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To determine the migration and invasion ability of the cells, 100 µL of Matrigel (BD354248; BD Biosciences, San Jose, CA, USA) was pipetted into ice-cold 300 µL serum-free medium with an ice-cold pipette and mixed well. An amount of 25 µL of the diluted Matrigel was added to the Transwell plate’s upper chamber (Costar; Corning Incorporated, Corning, NY, USA) and the entire polycarbonate film was coated at 37°C for 30 minutes to allow polymerization of Matrigel. Cells were digested with trypsin (Gibco, Thermo Fisher Scientific), washed with PBS, and resuspended in serum-free DMEM (D6046; Sigma Aldrich Co.). The cell density was adjusted to 0.5×106 cells/mL before plating in a 24-well Transwell upper chamber (Corning Incorporated). Medium containing 20% FBS (Gibco, Thermo Fisher Scientific) was added to Tran-swell lower chamber and the plate was incubated at 37°C for 24 hours. After incubation, the plate was washed twice with PBS, and methanol was for 30 minutes to fix the cells after which the plate was air dried. Transwell was then stained with crystal violet for 20 minutes and the relative migration was determined by counting the cells under the microscope.
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10

Culturing Immortalized Murine Macrophages

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Immortalised murine bone marrow-derived macrophages (iBMDM) were a gift from Prof. Douglas Golenbock (University of Massachusetts, USA). [45 (link)] iBMDM were cultured in Dulbecco’s Modified Eagle’s medium (DMEM) (D6046, Sigma Aldrich, Germany) supplemented with 10% Fetal Calf Serum (FCS) (SH3007003 Cytiva Hyclone, Thermo Fisher Scientific, Basingstoke, Hampshire, UK), 2 mM L-glutamine (59202C, Sigma Aldrich, Germany), 100 U/ml penicillin and 100 μg/ml streptomycin (Penicillin-Streptomycin P4458, Sigma Aldrich, Germany). iBMDMs were seeded in 96 well plates at 1 x 106 cells/ml unless otherwise stated.
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