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48 protocols using phosphate buffered saline (pbs)

1

Cell Culture Supernatant and Lysate Preparation

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After 96 h of incubation under each experimental condition, the cell culture supernatant was collected in ice-cold tubes. The cells were rinsed with phosphate-buffered saline (PBS; Takara Bio Inc., Shiga, Japan), mixed with 800 μL of RIPA buffer with PIC, detached from the 100 mm/Tissue Culture Dish by Cell Lifter (AS ONE Corporation, Osaka, Japan), and collected in ice-cold tubes. These cell lysates were homogenized and centrifuged at 10,000× g for 15 min at 4 °C; the supernatant was immediately dispensed in new ice-cold tubes. The samples were immediately frozen in liquid nitrogen and stored at −80 °C until they were examined for use in LC-EIS-MS, ELISA, or TBARS assay.
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2

Quantification of Thiol Compounds

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l-Cys, D,l-Hcy, l-GSH, CysGly, and γGluCys were purchased from Sigma-Aldrich (St. Louis, MO, USA). N-Acetyl-l-Cysteine (NAC), tiopronin (N-(2-mercaptopropionyl)glycine, MPG), and trichloroacetic acid (TCA) were obtained from Wako (Osaka, Japan). Ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate (SBD-F) was purchased from Dojindo (Kumamoto, Japan). TCEP was from Tokyo Chemical Industry (Tokyo, Japan). Phosphate buffered saline (PBS) was purchased from Takara Bio (Shiga, Japan). HPLC-grade acetonitrile was used. Water was purified using a Milli-Q system (Millipore, Bedford, MA, USA). All other chemicals were of analytical grade.
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3

Detailed Chemical Reagent Usage Protocol

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We purchased MMS and CDDP from Nacalai Tesque Inc (Kyoto, Japan), MMC from Sigma‐Aldrich Inc. (CA), and CP from FUJIFILM Wako Pure Chemical Co. (Tokyo, Japan). We purchased liver S9 prepared from SD rats treated with phenobarbital and 5,6‐benzoflavone from BoZo Research Center Inc (Tokyo, Japan). All test chemicals were dissolved in phosphate‐buffered saline PBS purchased from Takara Bio Inc. (Shiga, Japan). All test chemicals were prepared immediately before the TK test.
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4

Harvesting Bovine Cardiac Sarcocysts

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Cardiac muscles were collected from slaughtered cattle at slaughterhouses in Saitama Prefecture. Each muscle was cut into approximately 2 cm (length) × 5 cm (width) × 0.5 cm (thickness) sections. Sarcocysts were picked up using a needle under a stereomicroscope, and morphological observations were made under an optical microscope. Samples of 30–50 cysts with septa within each cyst, thin cyst walls (<1 µm thickness), and hair-like villar protrusions were collected in 1.5 mL tubes containing 200 µL sterile phosphate buffered saline (PBS) (TAKARA Bio Inc., Kusatsu, Japan). The samples were then centrifuged at 400 × g, washed three times with sterile PBS, and stored at 4°C until nucleic acid extraction.
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5

Quantification of Thiol-Containing Compounds

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L-Cys, D,L-Hcy, L-GSH, and CysGly were purchased from Sigma-Aldrich (St. Louis, MO, USA). Trichloroacetic acid (TCA) was obtained from Wako Pure Chemical (Osaka, Japan). Ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate (SBD-F) was purchased from Dojindo (Kumamoto, Japan). TCEP was purchased from the Tokyo Chemical Industry (Tokyo, Japan). Phosphate buffered saline (PBS) was purchased from Takara Bio (Shiga, Japan). HPLC-grade acetonitrile was used. Water was purified using a Milli-Q system (Millipore, Bedford, MA, USA). All other chemicals were of analytical grade.
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6

Amyloid-β Cytotoxicity Assay in HT22 Cells

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HT22 cells were seeded in 96-well plates at 3000 cells/well and incubated at 37 °C with 5% CO2 for 3 h [35 (link),36 (link)]. The cells in each well were transfected with 0.2 μg of the pEGFP-C1/Aβ42 plasmid (originating from Professor Junsoo Park, Yonsei University, Seoul, Korea) with Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA). After transfection for 10 h, the tested compounds dissolved in the medium were added to the seeded cells, and the cells were incubated for 24 h. Then, 20 μL of MTT solution (2 mg/mL) was added, and the cells were incubated for 3 h in the dark. The cells were subsequently washed with phosphate-buffered saline (PBS) (Takara, Kusatsu, Japan), and 100 mL of DMSO was added to solubilize formazan. The absorbance at 570 nm was measured with a microplate reader (VersaMaxTM, Randor, PA, USA). Fluorescence imaging was conducted by using a fluorescence microscope (Olympus ix70, Tokyo, Japan).
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7

Fetal Gonad Histological Analysis

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On GD 18, a total of 29 dams were euthanized with an overdose of sevoflurane (SevoFlot; DS Pharma Animal Health Co. Ltd., Osaka, Japan) and a total of 247 fetuses were collected via cesarean section (Table 1). Each fetus was assigned a unique identification number based on its location in the uterus following standard operating procedures and was humanely euthanized by submersion in ice-cold phosphate-buffered saline (PBS, pH 7.4; TaKaRa Bio Inc., Shiga, Japan). To visualize the implantation sites for counting, the empty uteri were clarified by immersing them in 0.2% NaOH (36) .
Fetal gonads were collected and fixed in 10% neutral-buffered formalin. Serial paraffin-embedded sections (4 lm thick) were prepared for hematoxylin and eosin (H&E) staining and for immunohistochemistry. Sections with the largest cross-sectional area were selected for use.
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8

Cellular Experimentation Reagents and Protocols

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All reaction reagents
and solvents were obtained
from Nacalai Tesque, Fujifilm Wako, Tokyo Chemical Industry, Kanto
Chemical, and Aldrich and used without further purification. Workup
and purification procedures were carried out with reagent-grade solvents
under air. Optical spectra were measured with spectroscopic grade
solvents. Deionized water (filtered through a 0.22 μm membrane
filter, R > 18.2 MΩ cm) was purified using
a Milli-Q system from Millipore.
The reagents for cellular experiments
were as follows: phosphate-buffered saline (PBS; TaKaRa), Dulbecco’s
modified Eagle medium (DMEM; Nacalai Tesque), FluoroBrite DMEM (Nacalai
Tesque), Opti-MEM I Reduced Serum Medium (Gibco), Trypsin-EDTA (Nacalai
Tesque), MG132 (Peptide Institute, INC.), bafilomycin A1 (Merck),
Lipofectamine 2000 (Invitrogen), MitoTracker Red (Thermo Fisher Scientific),
Transferrin-Alexa 594 (Thermo Fisher Scientific), LumiTracker Lyso
Red (LysoTracker-Red; Lumiprobe), 35 mm single-well glass-base dishes
(Iwaki), and Easy iMatrix-511 for laminin coating (Nippi).
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9

Imaging of Mandibles and Molars from Dmp1-EGFP Mice

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Mandibles and first molars were taken from Dmp1-EGFP neonatal mice and fixed overnight in 4% paraformaldehyde phosphate buffer solution (Wako Pure Chemical Industries, Ltd., Osaka). Fixed tissues were then decalcified with 10% ethylenediaminetetraacetic acid (EDTA) (MUTO PURE CHEMICALS Co., Ltd., Tokyo) for 1 week. After decalcification, they were dehydrated with a series (10%, 20%, 30%) of sucrose (Sigma-Aldrich Co. LLC, St. Louis) and phosphate buffered saline (PBS) (Takara Bio Inc., Shiga). Tissues were embedded in optimal cutting temperature compound (O.C.T., Sakura Finetek Japan Co., Ltd., Tokyo) and 10-μm sections were obtained using a cryostat (Leica, Wetzlar). Fluorescent imaging was performed using a fluorescence microscopy system (BZ-X700) (KEYENCE Corp., Osaka).
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10

IFN-γ Release Assay for Tuberculosis Diagnosis

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The 26 heparinized whole blood samples were used for the TB test, which was performed by IFN-γ release assay, as described previously [42 (link)]. Briefly, bovine purified protein derivatives (bPPD) (1000 international units per milliliter [IU/mL], diluted into 50 IU/mL) (China Institute of Veterinary Drugs Control, Beijing, China), avian purified protein derivatives (aPPD) (1000 IU/mL, diluted into 50 IU/mL) (China Institute of Veterinary Drugs Control, Beijing, China), Concanavalin A (ConA) (5 mg/mL, diluted into 100 μg/mL) (Sigma, California, USA) were used as the positive control, and phosphate-buffered saline (PBS) (10X, diluted into 1X) (Takara, Dalian, China) was used as the negative control to stimulate the whole blood overnight. Then, the supernatant plasma was collected and the IFN-γ concentration was measured using the standard curve of the IFN-γ according to the instructions of the commercial human/monkey IFN-γ quantification kit (MABTECH, Stockholm, Sweden). Based on the criteria previously established by this laboratory, a sample was classified as TB positive if the difference in the IFN-γ concentration between the bPPD- and aPPD-stimulated samples was equal to or greater than 114.5 pg/mL [43 (link)].
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