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32 protocols using c0775

1

SARS-CoV-2 Viral Plaque Assay

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Serum samples were diluted in DMEM, mixed with 80 TCID50 SARS-CoV-2, and incubated for 1 hour at 37°C. Serum/virus mixtures were then used to infect confluent Vero-E6 cells for 1 hour at 37°C. The serum/virus was then removed from cells and replaced with 0.3% agarose (MilliporeSigma, A9539) in DMEM/4% FBS and incubated for 72 hours at 37°C. Cells were then fixed with 4% paraformaldehyde in PBS and stained with 0.25% crystal violet (MilliporeSigma, C0775) in 20% ethanol/water for visualization of plaques.
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2

Anchorage-Independent Growth Assay

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For anchorage-independent growth assays, the volume ratio of the bottom well was 1.2% agar (MilliporeSigma, A5431)/2× RPMI 1640/FBS = 4.5:4.5:1, and the volume ratio of the top well was 0.8% agar/2× RPMI 1640/FBS = 4.5:4.5:1. Cells (1,000 LNCaP cells) were seeded on 6-well plates 36 hours after siRNA transfection. After 10–14 days, the colonies were captured using a microscope (SOPTOP, XD-T) equipped with a digital camera (TOUPCAM, E3ISPM12000KPA). Then the cells were washed with PBS and stained with 0.1% crystal violet (MilliporeSigma, C0775). The stained wells were washed with PBS, and the colonies were counted.
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3

Transwell Assay for BMDM Migration

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HASMCs were seeded in the lower chambers of a Corning Costar Transwell (6.5 mm diameter, 8.0 μm pore size, MilliporeSigma, CLS3464) plate and transfected with siControl or siBAF60c or infected with Ad-GFP or Ad-BAF60c. After 48 hours, the cells were incubated in fresh opti-MEM (Gibco, Thermo Fisher Scientific; 31985-070) with or without TNF-α (20 ng/mL) stimulation for 4 hours. The medium was subsequently changed to fresh opti-MEM. BMDMs were seeded in the upper chambers of the Transwells (105/chamber) and cocultured with HASMCs in the fresh opti-MEM. After 12 hours of coculture, the BMDMs on the upper surface of the Transwell insert were removed by scraping with a cotton swab, and the membranes were fixed in methanol for 30 minutes before staining with 0.1% crystal violet (MilliporeSigma, C0775) for 20 minutes at room temperature. Images of 4 random fields per Transwell were captured by microscopy, and the numbers of migrated cells were calculated using ImageJ software.
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4

Quantifying Colony-Forming Capacity in Osteoarthritis

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To evaluate the colony-forming unit (CFU) capacity, cSM-MPCs of normal (n = 8) and OA (n = 12) donors were plated in 58 cm2 Petri dishes (664160, CELLSTAR®, Greiner Bio-One) at three cell densities, i.e. ± 0.25-, 0.5-, and 1 × 103 cells/Petri dish (equivalent to ± 4-, 8-, and 17 cells/cm2). After 10–14 days in humidified, normoxic conditions (5% CO2/21% O2) at 37 °C, normal culture conditions, cells were stained with 0.5% crystal violet (C0775, Sigma-Aldrich) in 100% methanol (MC1060092511, Merck Millipore) for 30 min. Colonies containing > 50 cells were counted in the appropriate plating density, i.e. the density wherein the individual colonies were not overlapping, and displayed as the percentage of the total seeded cell number.
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5

Crystal Violet Staining Protocol

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Following treatment, the cells were washed twice with PBS and fixed with cold 100% methanol for 5 min at −20°C. After being washed twice with PBS, the cells were stained with 0.1% crystal violet solution (C0775; Sigma-Aldrich; Merck KGaA, Darmstadt, Germany) for 5 min at room temperature. The cells were then washed 5 times with distilled water and observed under a microscope (Ti-S; Nikon). The results were analyzed using ImageJ software (version 1.8.0).
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6

Colony Formation Assay with PANC-1 Cells

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Equal numbers of PANC-1 or PANC-1R cells (1000/well) were seeded into 6-well plates and cultured for 2 weeks in the medium. After washing with phosphate-buffered saline (PBS), the cells were fixed with 4% paraformaldehyde for 30 min and stained with 0.1% crystal violet (C0775, Sigma-Aldrich) for 30 min at room temperature. The number of colonies was counted under a light microscope.
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7

Cell Viability Assays in Normogravity and Microgravity

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Cell viability after normogravity and microgravity treatments was assessed with Clonogenic Assay and Trypan Blue Exclusion Assay. In the colony assay, at the end of treatments, cells (5 × 102) were plated in 100 mm dishes in culture medium with 10% FBS to perform the clonogenic assay. At the end of treatments, plates were washed twice with a phosphate buffered saline solution (PBS; 79382; Sigma-Aldrich–MERCK, St. Louis, MO, USA) and fixed with 4% formaldehyde solution in PBS (F8775; Sigma-Aldrich–MERCK, St. Louis, MO, USA) at rt. After 20 min, dishes were washed twice in PBS and stained for 5 min with 0.5% crystal violet (C0775; Sigma-Aldrich–MERCK, St. Louis, MO, USA). Finally, cells were washed with distilled water and air-dried. The colonies were counted the following day. In trypan blue exclusion assay, cells were harvested and stained with 0.4% trypan blue (T8154; Sigma-Aldrich–MERCK, St. Louis, MO, USA). The cell suspension was applied to a haemocytometer and counted with a phase contrast microscopy (NIKON Eclipse TE2000U, Nikon Netherlands, Amsterdam, The Netherlands).
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8

Clonogenic Assay for LINC00665 and miR-339-3p

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After transfection with siLINC00665, miR‐339‐3p mimic, or miR‐339‐3p inhibitor or co‐transfection with siLINC00665 and miR‐339‐3p inhibitor, A375 cells and A2058 cells were detached by Trypsin (9002‐07‐7, Sigma‐Aldrich) and plated at 1 × 105 cells/per well in 6‐well plates, respectively. Then, the cells were allowed to clone at 37°C for 2 weeks, after which colonies were washed with phosphate‐buffered saline (PBS; P5493, Sigma‐Aldrich), fixed in 4% paraformaldehyde (P6148, Sigma‐Aldrich) for 15 min, and stained with 0.1% crystal violet (C0775, Sigma‐Aldrich) for 10 min. The number of colonies with diameters of longer than 1.5 mm in six randomly selected fields was counted under microscope (IX71; Olympus).
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9

Quantifying cell migration and invasion

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In vitro migration and invasion assay was performed in 24-well plates using 8.0-µm pore polycarbonate trans-well inserts (BD Corning). 5 × 104 cells were suspended in serum-free DMEM and overlaid in the upper chamber of each trans-well. DMEM medium containing 10% FBS was added to the lower chamber as a chemoattractant. The inserts were then incubated at 37 °C in a humidified atmosphere containing 5% CO2. After 36 and 48 hours of incubation, cells that failed to penetrate the pores of the filter were removed by cotton swabs and the migrated cells were fixed and stained with 0.1% crystal violet (C0775, SIGMA, USA). Images of crystal violet stained cells were acquired with the help of an IX-70 inverted microscope (Olympus, Tokyo, Japan) equipped with a digital camera. Quantification of migrated cells from at least 5 different microscopic fields per sample was done using ImageJ 1.48 v software. The migratory activity was calculated as the average number of migrated cells in each assay from three independent experiments. Further, migratory activity was also assayed by dissolving cells that invaded the filter in methanol and measuring absorbance at 570 nm using a spectrophotometer.
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10

Cell Viability Assessment via CCK-8 and Crystal Violet

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Cell Counting Kit‐8 (CCK‐8: Dojindo Laboratories, Rockville, MD, USA) assay was used to assess cell viability. Cells were seeded in 6‐well plates starting at 2 × 105 cells per well and incubated for 24 h. After siRNA transfection for 48 h, a mixture of CCK‐8 solution and RPMI‐1640 medium supplemented with 10% FBS was added to each well and incubated in 5% CO2 at 37 °C for 10 min. The absorbance at 450 nm was assessed by a microplate reader. For crystal violet staining, the cells were fixed with cold 100% methanol for 5 min at −20 °C and stained with 0.1% crystal violet solution (C0775, Sigma‐Aldrich, Merck KGaA, Darmstadt, Germany) for 5 min at room temperature after siRNA transfection for 48 h. Then, the cells were observed under a microscope (CELENA® S Digital Imaging System, Logos Biosystems, Anyang, Korea).
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