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25 protocols using paraformaldehyde solution

1

Immunofluorescence Staining of EGFR and NK1R

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A total of 1 × 104 cells were plated in a glass bottom/confocal petri dish (Biosharp, Hefei, China) and cultured overnight. Cells were fixed by 4% paraformaldehyde solution (Beyotime) for 10 min and blocked with immuno-staining blocking buffer (Beyotime) for 60 min at room temperature, then incubated with mouse anti-EGFR (ProteinTech, 66455-1-lg) and rabbit anti-NK1R (Abcam, ab183713) overnight at 4 °C. The cells were then stained with coralite594-conjugated anti-rabbit IgG (ProteinTech, SA0013-4) and coralite488-conjugated anti-mouse IgG (ProteinTech, SA0013-1) for 2 h at room temperature. Nuclei were stained by DAPI (1 μg/ml, Sangon). Fluorescent images were captured by a microscope equipped with a laser-scanning confocal imaging system (Zeiss LSM800, German).
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2

Micro-CT Analysis of Rat Ankle Bone Damage

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To evaluate bone damage, the left ankle joints of rats sacrificed at day 35 were fixed in 4% paraformaldehyde solution (Beyotime) and scanned in an ex vivo micro-CT machine (Skyscan1174 X-ray Micro-CT) (Bruker) for 160 min at 50 kV and 800 μA with a resolution of 14.5 μm. The dataset was then reconstructed using N-Reconn and CTvox software to obtain three-dimensional images of the joints and to measure bone mineral density (BMD) and other morphometric parameters. The left calcaneus in the rats was assessed for bone destruction, and its BMD was measured as a comparative indicator of bone damage. The highlighted ROI in the left calcaneus was analyzed for the following morphometric parameters 53 (link): (1) bone volume/total tissue volume (BV/TV), (2) trabecular number (Tb.N), (3) trabecular thickness (Tb.Th), (4) trabecular separation (Tb.Sp), and (5) trabecular mesh factor (Tb.Pf).
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3

Silk Fibroin-Reinforced PLLA Scaffolds

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Poly-l-lactic acid (PLLA, Mw: 50 000, Daigang Biomaterial, Jinan,
China); methylene chloride (Fengchuan Chemical Reagent Co., Tianjin,
China); ammonium bicarbonate (Adamas-β, Shanghai, China); poly(vinyl
alcohol) (PVA, Sinopec Chongqing Svw Chemical Co., Chongqing, China);
NaOH (Fengchuan Chemical Reagent Co., Tianjin, China); and degummed
silk and SF (Beijing Sinolactide Medical Technology Company, China).
Gelatin (Macklin, Shanghai, China); carbodiimide (EDC) (Aladdin, Shanghai,
China); type IV collagenase (Sigma-Aldrich, MO); high-glucose Dulbecco’s
modified Eagle’s medium (H-DMEM, Gibco, CA); fetal bovine serum
(FBS, Gibco, CA); penicillin–streptomycin–neomycin antibiotic
mixture (PSN, Gibco, CA); LIVE/DEAD Viability/Cytotoxicity Kit (Thermo
Fisher, CA); CCK-8 solution (Beyotime, Shanghai, China); TRIzol reagent
(Thermo Fisher, CA); Go Taq qPCR and RT-qPCR systems (Promega); SYBR
Green Kit (Roche, Germany); 4% paraformaldehyde solution (Beyotime,
Shanghai, China); sucrose (Sigma, MO); optimum cutting temperature
(OCT) compound (Sakura, Japan); anti-collagen I antibody (Abcam, U.K.);
anti-collagen II antibody (Abcam, U.K.); secondary antibody (Solarbio,
Beijing, China); and DAB detection kit (Solarbio, Beijing, China).
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4

TUNEL Assay for Macrophage Apoptosis

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One milliliter of THP-1 cells at 3 × 105 cells/mL density was seeded, differentiated by PMA, and infected with engineered Msmg-2387 or Msmg-EV strains (MOI = 10) for 24 h. TUNEL staining was analyzed via a one-step TUNEL kit (Beyotime, China). In brief, macrophages were washed two times and fixed in a 4% paraformaldehyde solution (Beyotime, China) for 0.5 h. Next, the macrophages were permeabilized with 0.2% (v/v) Triton X-100 solution for 20 min and stained with the TUNEL working solution for 1 hour. At last, macrophages were stained with DAPI solution for 8 min in the dark. The images were obtained through a fluorescence microscope.
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5

Colony Formation Assay Protocol

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After corresponding transfection and/or treatment, cells were cultivated into a 6-well plate with 500 cells/well for two weeks. Then, cells were rinsed by PBS, fixed with 4% paraformaldehyde solution (Beyotime Biotechnology), and dyed using Giemsa solution (Solarbio, Beijing, China). The colony number of each group was counted under a microscope.
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6

Transwell Assay for Cell Migration and Invasion

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Cell migration was determined using a modified two-chamber transwell assay (Corning Incorporated, USA). Briefly, after relevant transfection, 1 × 103 GH3 cells were suspended in 200 μL serum free-DMEM and added into the upper chamber. Complete DMEM (600 μL) was added into the lower chamber. After incubation at 37°C for 48 h, cells were immediately fixed with 4% paraformaldehyde solution (Beyotime Biotechnology, China). Then, non-migrated cells in the upper chamber were removed carefully using a cotton swab and migrated cells in the lower chamber were counted under a microscope (Nikon, Japan). Cell migration (%) was calculated by average number of migrated cells in transfection group / average number of migrated cells in control group × 100%.
Cell invasion was evaluated similarly with cell migration, except that the transwell membrane was pre-incubated using Matrigel (BD Biosciences, USA). Cell invasion (%) was calculated by average number of invaded cells in transfection group / average number of invaded cells in control group × 100%.
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7

Quantifying Cell Invasion Ability

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To measure the cell invasion ability, transwell chambers (8-μm pore size) were coated with Matrigel (50 μL/well with a solution containing four volumes of serum-free medium to one volume of Matrigel solution) in 24-well plates. Cell migration assay was performed with transwell chambers (8-μm pore size) coated with serum-free medium in 24-well plates. Cells at a density of approximately 1.5 × 105 cells/well were seeded into the upper chamber of the insert. After incubation for 48 h at 37 °C with 5% CO2, any cells that had invaded the lower cavity were fixed by 4% paraformaldehyde solution (Beyotime, Cat no: P0099) for 10 min and then stained with 5% crystal violet solution (Beyotime, Cat no: C0121) for 10 min. The cells were counted in three randomly selected visual fields using an inverted microscope (IX71, Olympus). The quantification analysis was carried on using the Image J software (Fiji Software). Cell numbers were counted at random three views, the average number of migratory and invasive cells were shown as histogram, respectively. All the experiments, including the quantification analysis, were performed in triplicate.
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8

Clonogenic Assay in Transfected Cells

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Transfected SW480 and RKO cells (300 cells/well) were added to 12-well plates. Then, SW480 and RKO cells were cultured for two weeks. Fresh medium was changed every 2 days during cell culture. After macroscopic cell clones appeared, PBS was employed to wash cells twice. Next, 4% paraformaldehyde solution (Beyotime, China) was utilized to fix cells for 20 min. Subsequently, crystal violet solution (Beyotime, China) was added to stain cells for 30 min. Finally, a camera (canon EOS 600d, Japan) was applied to photograph and count the number of cell clusters.
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9

Cytotoxicity Assessment of SN38 in Cancer Cells

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Dopamine hydrochloride (purity = 99%), SN38 (98%), dimethyl sulfoxide (DMSO), ammonia (28–30%), 3H-Indolium,5-[[[4-(chloromethyl)benzoyl]amino]methyl]-2-[3-(1,3-dihydro-3,3-dimethyl-1-octadecyl-2H-indol-2-ylidene)-1-propenyl]-3,3-dimethyl-1-octadecyl-,chloride (CM-Dil), fluorescein isothiocyanate (FITC), phenylmethylsulfonyl fluoride (PMSF), deionized water (pH 7.0) and absolute ethanol (99.8%) were purchased from Sigma-Aldrich (Saint Louis, MO, USA). Dulbecco’s modified Eagle’s medium (DMEM) with high glucose, Minimum Essential Medium α (MEM α), and fetal bovine serum (FBS) was obtained from Thermo Fisher Scientific (Waltham, MA, USA). RIPA lysis buffer, a bicinchoninic acid (BCA) protein kit, enzyme-linked immunosorbent assay (ELISA) kit for tumor necrosis factor (TNF)-α, 4% paraformaldehyde solution, 4′,6-diamidino-2-phenylindole (DAPI), Triton X-100, and Coomassie Brilliant Blue were purchased from Beyotime (Shanghai, China). Other reagents were of analytical grade and purchased from Beijing Chemical Reagents Company (Beijing, China) unless stated otherwise.
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10

Immunohistochemical Analysis of Nrf2, 4-HNE, and GPX4

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Lung tissues were fixed in 4% paraformaldehyde solution (Beyotime, China) for 24 h and then dehydrated and embedded in paraffin following routine methods. The slides were rinsed with Bond Dewax Solution at 72 °C to deparaffinize the tissue slices. Then, the sections were treated with Enhanced Endogenous Peroxidase Blocking Buffer (Beyotime) for 5 min to block endogenous peroxidase activity before they were incubated with Nrf2 antibody (1:500 dilution, Abcam, USA), 4-HNE antibody (1:200 dilution, Abcam) or GPX4 antibody (1:500 dilution, Abcam) overnight, after which DAB was quickly added. The color rendering time was controlled for 5 min. Images viewed under an Olympus microscope were captured. The Nrf2 immunostaining results were scored by multiplying the percentage of positive cells (0, <10%; 1+, 10–25%; 2+, 25–50%; 3+, 50–75% or 4+, >75%) by the staining intensity (0, negative; 1+, weak; 2+, moderate; or 3+, strong), and the 4-HNE and GXP4 immunostaining results were scored as the integrated optical density (IOD)/area as detected by Image-Pro Plus.
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