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98 protocols using phosphate buffered saline (pbs)

1

Isolating Exosomes from Human Plasma

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Primers and phosphate-buffered saline (PBS) were purchased from Sangon Biotech Co., Ltd. (Shanghai, China). Fe3O4@TiO2 was obtained from Nanjing Xiuyuan Biotechnology Co., Ltd. (Jiangsu, China). Monoclonal anti-CD63 antibody, monoclonal calnexin antibody, and monoclonal TSG101 antibody were purchased from Abcam Co., Ltd. (Shanghai, China). A solution of 28 wt% ammonium hydroxide (NH3•H2O) and PKH26 Red Fluorescent Cell Linker Mini Kit were obtained from Sigma Co., Ltd. (Shanghai, China)., A 0.22-μm syringe-driven filter was purchased from Millipore (United States). Deionized water was processed by Ultrapure Millipore water (18.2 MΩ cm). High glucose Dulbecco’s modified Eagle’s medium (DMEM) and penicillin–streptomycin solution were purchased from Hyclone (UT, United States). Exosome-depleted fetal bovine serum (FBS) media supplement was purchased from System Biosciences, SBI (CA, United States).
All cell lines were purchased from the Shanghai Cell Bank, Chinese Academy of Sciences (Shanghai, China). Healthy human and lung cancer patient plasma samples were supplied by Nanjing University-affiliated Drum Tower Hospital. The samples were centrifuged at 1,500 g for 10 min at 4°C. The supernatant was collected and centrifuged at 2,000 g for 10 min at 4°C to remove platelets. The supernatant was centrifuged at 15,000 g for 30 min and stored at −80°C.
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2

Cell Membrane Integrity Evaluation

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To evaluate cell membrane integrity after quenching, the cells after quenching were stained with fluorescent dyes SYTO 9 (Invitrogen, Carlsbad, USA) and propidium iodide (PI) (Invitrogen). The quenched cell pellets were washed twice with sterile phosphate-buffered saline (PBS) (Sangon Biotech, Shanghai, China) and resuspended in 2 ml of PBS. Cell suspensions (1 ml) were diluted by adding 20 ml of PBS and incubated at 30°C for 1 h, mixing every 15 min. The incubated cell pellets were washed twice and resuspended in 10 ml of PBS. Equal volumes of SYTO 9 and PI were added to the bacterial suspension at a final concentration of 3 μl/ml, and the mixture was incubated at room temperature in the dark for 15 min. The stained bacterial suspension (5 μl) was pipetted onto a glass slide and covered with a coverslip. The stained, quenched cells were visualized by confocal laser scanning microscopy (Nikon A1R MP, Tokyo, Japan) with a 543-nm He-Ne laser (red channel) and a 488-nm Ar laser (green channel).
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3

Antimicrobial Activity Assay Protocol

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Luria–Bertani (LB) broth powder was purchased from Meilunbio (Dalian, China). 666-15 was purchased from Topscience (Shanghai, China). Antibiotics were purchased from MedChem Express (MCE, United States). Thiazolyl blue tetrazolium bromide (MTT) and phosphate-buffered saline (PBS) were purchased from Sangon Biotech (Shanghai, China). The bacterial total RNA extraction kit and DNA extraction kit were purchased from TIANGEN (Beijing, China). RT Master Mix and SYBR Green qPCR Master Mix were purchased from MedChem Express (MCE, United States). The lipopolysaccharide (LPS) detection kit was purchased from Cloud-Clone (Wuhan, China). Propidium iodide (PI) was purchased from Thermo Fisher Scientific, USA. 3,3-Dipropylthiadi-carbocyanine iodide [DiSC3(5)] was purchased from AAT Bioquest, USA. The LIVE/DEAD BacLight bacterial viability kit was purchased from Invitrogen, USA.
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4

Baicalein Preparation and Storage

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Baicalein was purchased from Aladdin (product number B107323, Shanghai Aladdin Biochemical Technology Co., Ltd., Shanghai, China). According to baicalein's product specification, we can get that its formula weight is 270.24 g/M and its purity is no less than 98%. We dissolved the baicalein in phosphate-buffered saline (PBS, Shanghai Sangon Biotech Co., Ltd., Shanghai, China) to make stock solutions and stored them at −20°C.
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5

Monkeypox Virus Quantification in Vero Cells

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The Vero E6 monolayer grown in a T225 flask was infected with MPXV at 0.5 multiplicity of infection (MOI). After that, cells were incubated at 37 °C with 5% CO2 for four days and analyzed under a microscope. After discarding the supernatant, the cells were washed with phosphate-buffered saline (PBS, Sango Biotech, Shanghai, China), and lysed by performing 3 freeze–thaw cycles at −80 °C. Then, the supernatants were collected by centrifuging at 3000 rpm for 5 min. To determine the virus concentration, a 10-fold serially diluted stock virus (supernatant) was added to the 96-well plate with 2~3 × 104 Vero cells per well prepared one day before. Cells were examined under a microscope for cytopathological effects after 5 days of culture at 37 °C, 5% CO2. Virus titer was determined by the method of Karber to determine the 50% cell culture infective dose (CCID50) [14 (link),15 (link)].
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6

NLRP3 Inflammasome Activation in J774A.1 Macrophages

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J774A.1 (Procell CL-0370) was kindly provided by Procell Life Science & Technology Co., Ltd., Wuhan, China. The cells were grown in RPMI 1640 medium (Gibco, Thermo Fisher Scientific, United States) supplemented with 10% fetal bovine serum (Premium, Pan Biotech, Germany) and 1% penicillin-streptomycin antibiotic (Gibco, Thermo Fisher Scientific).
For inducing NLRP3-inflammasome activation, cells were primed with LPS (500 ng/ml, Sigma-Aldrich, United States) for 6 h in the presence or absence of CAN (10 μM, Biochempartner). Inhibitors used in the study (if any) were also added simultaneously with LPS and CAN. Then, stimulated with ATP (5 mM, Sigma-Aldrich, United States) for 30 min.
The supernatant was collected for either the enzyme-linked immunosorbent assay (ELISA) or western blotting experiments after being concentrated in ultrafiltration centrifuge tubes (3 kDa, Merck, Germany). Cells were washed twice with ice-cold phosphate-buffered saline (Sangon Biotech), and 1 ml of RNA isolation reagent (TRIzol, Invitrogen, Thermo Fisher Scientific) or 80 μl of lysis buffer [50 mM Tris (Sangon Biotech), 150 mM NaCl (Sangon Biotech), 0.1% (w/v) sodium dodecyl sulfate (Sangon Biotech), 1% Triton X-100 (Sangon Biotech), and 1 tablet/50 ml Protease Inhibitor Cocktail (Roche), pH 8.0] was added for cell RNA or protein extraction, respectively.
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7

Polymeric Nanoparticle Formulation and Characterization

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PEG5,000-PLGA (LA:GA ratio 50:50; molecular weight: 50 kDa) was purchased from Jinan Daigang Biomaterial Co Ltd (Jinan, People’s Republic of China [PRC]). Polyvinyl alcohol (PVA) was purchased from Sigma-Aldrich (St Louis, MO, USA). DAPI (4′,6-diamidino-2-phenylindole) was purchased from Hoffman-La Roche Ltd (Basel, Switzerland), and MTT was purchased from Solarbio (Beijing, PRC). MitoTracker green FM and LysoTracker green FM were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Paraformaldehyde and phosphate-buffered saline (PBS) were purchased from Sangon (Shanghai, PRC). Penicillin–streptomycin, fetal bovine serum, trypsin–ethylenediaminetetraacetic acid, Modified Eagle’s Medium (MEM), and Dulbecco’s MEM (DMEM) for cell culture were purchased from HyClone (South Logan, UT, USA). Deionized water was obtained using the Barnstead Nanopure water-purification system from Thermo Fisher Scientific. All other chemicals and reagents used were of analytical grade and obtained commercially unless stated otherwise.
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8

Histological Analysis of Mouse Testis

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Mouse testicular and epididymal samples were collected, washed three times with phosphate-buffered saline (PBS; Sangon, Shanghai, China), fixed in paraformaldehyde (Servicebio, Wuhan, China), and embedded in paraffin (Sangon, Shanghai, China). The 5-μm sections were dewaxed and rehydrated and then stained with haematoxylin (Servicebio, Wuhan, China) solution for 3–5 min., Followed by staining with eosin (ServiceBio, Wuhan, China) for 3 min. The sections were dehydrated in 85% ethanol (Sangon, Shanghai, China) and 95% ethanol for 5 min. The sections were then dehydrated three times in 100% ethanol for 5 min each and sealed with neutral balsam (Sangon, Shanghai, China).
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9

Quantifying Apoptosis by Flow Cytometry

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To determine the occurrence of apoptosis within 72 h of transfection, cells were harvested using trypsinization (Sigma-Aldrich) and rinsed twice with phosphate-buffered saline (Sangon Biotech). Cells were then centrifuged (4°C, 1,000 ×g) for 10 min. Cells were resuspended in 200 μl binding buffer (Sangon Biotech) and treated with 10 μl Annexin V-fluorescein isothiocyanate (FITC) and 5 μl propidium iodide (PI; both Sigma-Aldrich) for 15 min at room temperature. The rate of apoptosis was then determined using flow cytometry (Epics-XL; Beckman-Coulter, Shanghai, China).
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10

Colorimetric Assay for Cell Viability

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Phosphate-buffered saline (PBS, pH = 7.4) and a Cell Counting Kit-8 (CCK-8) were purchased from Sangon Biotech Co., Ltd. (Shanghai, China). Dulbecco’s modified Eagle’s medium (DMEM) and penicillin–streptomycin solution were purchased from HyClone (Logan City, UT, USA). Fetal bovine serum (FBS) was purchased from PAN-biotech (Aidenbach, Germany). The human lung adenocarcinoma cancer cell line A549 was purchased from Silver Amethyst Biotech. Co., Ltd. (Beijing, China). All reagents and buffers were autoclaved and used under aseptic conditions. The CCK-8 assay was performed using a microplate reader (EP0CH2, Suzhou Xitogen Biotechnolgies Co., Ltd., Suzhou, China).
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