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33 protocols using methanol

1

CXCR4 Expression Analysis in Corneal Tissue

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Corneas were cut and fixed in 10% neutral buffered formalin (Beijing Yili Fine Chemicals Co., Ltd.; Beijing, China) for 24 h. Paraffin-embedded tissue sections (4 μm) were deparaffinized, rehydrated, and treated with 0.3% hydrogen peroxide in methanol (Beyotime Institute of Biotechnology, Inc., Haimen, China) for 30 min, to eliminate endogenous peroxidase activity. The tissue sections were incubated for 60 min at room temperature with rabbit anti-mouse CXCR4 polyclonal antibody (1:200 dilution; cat. no. ab2074; Abcam). Following three washes of 3 min with phosphate-buffered saline (PBS; Beyotime Institute of Biotechnology, Inc.), a 3,3′-diaminobenzidine detection kit (PV9000; ZSGB-BIO, Beijing, China) was used for CXCR4 staining, according to the manufacturer's protocols. Images were captured with the Leica DM4000B biological microscope equipped with a Leica DFC 550 digital camera and Leica Application Suite version 4.2.0 software (Leica Microsystems GmbH, Wetzlar, Germany).
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2

Transwell-Based Cell Migration and Invasion Assay

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The cellular migration assay was assessed using Transwell chambers with a pore size of 8 µm (Corning Incorporated, Cambridge, MA, USA). Following transfection for 48 h, 5×104 transfected cells (miR-592 and NC) in 300 µl medium without FBS were seeded into the upper chamber of the Transwell, while 500 µl medium supplemented with 20% FBS was placed into the lower chamber. For the Matrigel invasion assay, the Transwell chamber was coated with Matrigel (BD Biosciences, San Jose, CA, USA). A total of 5×104 transfected cells (miR-592 and NC) in 300 µl medium without FBS were seeded into the upper chamber of the Transwell, while 500 µl medium supplemented with 20% FBS was placed into the lower chamber. Cells were incubated at 37°C for a further 24 h for the migration assay and 48 h for the invasion assay. In the two assays, the cells were fixed with 100% methanol for 5 min (Beyotime Institute of Biotechnology, Haimen, China) and stained with 0.5% crystal violet (Beyotime Institute of Biotechnology) for 5 min. Following this, cells remaining on the upper surface of the membranes were removed carefully using cotton swabs. The migrated and invaded cells were then counted in five randomly selected fields with an inverted microscope (Olympus Corporation, Tokyo, Japan). Each experiment was repeated ≥times.
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3

Cell Invasion Assay using Transwell System

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Transwell inserts (Costar; Corning, Inc.) precoated with Matrigel (BD Biosciences) were used to examine cell invasion. In total, ~105 transfected HTR-8/SVneo cells were inoculated in the upper well in 250 µl RPMI 1640 medium, whereas the lower well contained 500 µl RPMI 1640 medium supplemented with 10% FBS (Sigma-Aldrich; Merck KGaA). After a 24-h incubation at 37°C with 5% CO2, non-invasive cells attached to the upper side of membranes were removed using cotton swabs. The invasive cells were fixed with 100% methanol (Beyotime Institute of Biotechnology) for 20 min at 37°C and stained with 0.1% crystal violet (Beyotime Institute of Biotechnology) for 10 min at 37°C. Stained cells were photographed and counted in five randomly-selected fields of view using a light microscope (DMI6000 B microscope; Leica Microsystems GmbH; magnification, ×200).
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4

Cell Migration and Invasion Assay

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Cell migration and invasion were revealed using transwell chamber (8.0 µm) without and with Matrigel (Corning, Madison, New York, USA), respectively. In brief, cells were mixed with FBS-free DMEM (Biosun) and then added into upper chamber of 24-well plate. DMEM contained 15% FBS was placed into lower chamber. After 24 h, supernatant was discarded and cells were washed using phosphate buffer solution (PBS) (Thermo Fisher). Then methanol (Beyotime) and crystal violet (Beyotime) were severally employed to immobilize and stain cells. The migratory and invasive abilities were determined by counting cell numbers with microscope (Olympus, Tokyo, Japan) with a 100( ×) magnification.
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5

Quantifying Cell Proliferation and Clonogenicity

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For the cell proliferation assay, 2×103 A549 cells/well were seeded into 96-well plates in triplicate. Cell proliferation was analyzed using a Cell Counting Kit-8 (CCK-8; cat. no. A311; Vazyme Biotech Co., Ltd.) assay, according to manufacturer's protocol. Briefly, cells were plated and incubated for 24 h in 96-well plates prior to test, 10 µl CCK8 solution was added to each well and incubated at 37°C for 2 h. The optical density (OD) was read at an absorbance of 450 nm using a multifunction microplate reader (Safire, TECAN) for 4 continuous days.
For the colony formation assay, 500 viable A549 cells per well were seeded into 6-well plates in triplicate. Following incubation at 37°C for 10 days, the colonies were fixed with methanol at room temperature for 30 min, stained with 0.05% crystal violet (Beyotime Institute of Biotechnology) for 60 min at 25°C, washed with running water to remove the excessive dye and imaged with an Epson Perfection V550 Photo scanner (Seiko Epson Corporation). Number of colonies (>50 cells) was calculated using ImageJ software version 1.45 (National Institutes of Health, Bethesda, MD, USA).
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6

Colony Formation Assay Protocol

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Transfected SGC-7901 cells undergoing exponential growth were trypsinized, harvested, and added to 6-well plates, which were incubated for 2 weeks. When a single cell colony contained ≥50 cells, the 6-well plates were removed for staining. After washing in PBS, colonies containing >50 cells were fixed in methanol (Beyotime, Shanghai) and stained with crystal violet (Solarbio, Beijing). After the 6-well plates were completely dry, photos were taken.
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7

Transwell Assay for Cell Migration and Invasion

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Cellular migration and invasion were assessed using Transwell chambers with a pore size of 8 µm (Corning Inc., Corning, NY, USA). Following transfection for 48 h, 5×104 transfected cells in 300 µl medium without FBS were seeded into the upper chamber, while 500 µl medium supplemented with 20% FBS was placed into the lower chamber. For the Matrigel invasion assay, the Transwell chamber was coated with Matrigel (BD Biosciences, San Jose, CA, USA). A total of 5×104 transfected cells in 300 µl medium without FBS were seeded into the upper chamber of the Transwell, while 500 µl medium supplemented with 20% FBS was placed into the lower chamber. Cells were incubated at 37°C for a further 24 h for the migration assay and 48 h for the invasion assay. In the two assays, the cells were fixed with 100% methanol for 5 min (Beyotime Institute of Biotechnology, Haimen, China) and stained with 0.5% crystal violet (Beyotime Institute of Biotechnology) for 5 min. Subsequently, cells remaining on the upper surface of the membranes were removed carefully using cotton swabs. The migrated and invaded cells were then counted in five randomly selected fields with an inverted microscope (magnification, ×200). Each experiment was repeated three times.
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8

Transwell Assay for Cell Invasion

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This assay was performed according to the published methods [24 (link)]. After 48 h of cell transfection, KYSE150 and TE-1 cells were diluted in serum-free RPMI-1640 medium and added into the upper wells of 24-well transwell chambers with Matrigel (Costar, Shanghai, China). RPMI-1640 medium containing 20% FBS was added to the lower chambers. Twenty-four hours later, the cells adhering to the lower chambers were fixed using methanol (Beyotime) and quantified under a high-power (100x) microscope (Olympus).
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9

Cell Proliferation and Migration Assay

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The CCK8 assays (Dojindo, Kumamoto, Japan) were used for accessing the ability of cell proliferation. The colon cancer cells were transfected with miRNA, siRNA, or control. After transfection, the cells were plated in 96-well plates. The CCK8 assays were conducted at 24, 48, 72, and 96 h. All the procedures were performed according to the manufacturer’s protocol. For the migration assays, the lower chamber of the Transwell inserts (Corning, Corning, NY, USA) was covered by Matrigel matrix (BD, Franklin Lakes, NJ, USA). Then transfected cells with no serum medium were plated into the upper inserts. The lower chambers were surrounded by 10% FBS medium (Gibco). The invaded cells were fixated with methanol (Beyotime, Beijing, China) and stained with 0.1% crystal violet (Beyotime) after 48 h. The invaded cells were counted in 10 randomized fields.
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10

Transwell Invasion Assay for Cell Motility

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Cell migration and invasion were investigated by transwell chambers (Millipore). Specially, the chambers were pre‐incubated with Matrigel (Corning) to reveal cell invasive ability. Briefly, cells were homogenized in serum‐free DMEM (Procell) and placed into the upper chambers. DMEM containing 15% FBS (Procell) was added into the lower chambers. After 24 h, the cells were incubated with methanol (Beyotime) and crystal violet (Beyotime), respectively. Results were confirmed by figuring up the number of cells in the lower chambers with an Eclipse Ts2R inverted microscope (Nikon) at a × 100 magnification.
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