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20 protocols using rankl

1

Osteoclastogenesis Assay with Modulators

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CD14+ cells were cultured for 10 days in 96-well flat-bottom plates under the following conditions: (i) 50 ng ml−1 M-CSF (BioLegend, San Diego, CA, USA) and 125 ng ml−1 RANKL (BioLegend); (ii) 50 ng ml−1 M-CSF and 5 µg ml−1 anti-RANKL Ab (R&D Systems, Minneapolis, MN, USA) with or without 10 ng ml−1 IL-8 (PeproTech, Rocky Hill, New Jersey, USA); and (iii) 50 ng ml−1 M-CSF, 125 ng ml−1 RANKL and 50 ng ml−1 TNF-α (BioLegend) with or without 3 ng ml−1 FK506. After culture, the number of OCLs per well was counted for each culture condition. Ten days after culture, cells were washed with phosphate-buffered saline (PBS), supplied with fresh media and cultured again overnight under the following conditions: (i) no medication, (ii) anti-RANKL Ab (5 µg ml−1) and (iii) anti-RANKL Ab (5 µg ml−1) and FK506 (3 ng ml−1). Media were collected from overnight cultures and cryopreserved at −30°C.
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2

Intestinal Organoid Culture with Jagged-1

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Following crypt isolation, the single cell suspension was resuspended in Matrigel (BD Bioscience) with 1μM Jagged-1 peptide (Ana-Spec). Roughly 300 crypts embedded in 25μl of Matrigel were seeded onto each well of a 24-well plate. Once solidified, the Matrigel was incubated in 600μl culture medium (Advanced DMEM/F12, Invitrogen) with streptomycin/penicillin and glutamatax and supplemented with EGF (100 ng/mL, Peprotech), R-Spondin-1 (600ng/mL, R&D), Noggin (100ng/mL, Prepotech), Y-276432 dihydrochloride monohydrate (10μM, Tochris), N-acetyl-1-cysteine (1μM, Sigma-Aldrich), N2 (1X, Life Technologies), B27 (1X, Life Technologies) and Wnt3A (25ng/mL, R&D Systems). Fresh media was replaced on day 3, and organoids were passaged by dissociation with TrypLE and resuspended in new Matrigel on day 6 with a 1:3 split ratio. For selected experiments, organoids were additionally treated with RANKL (100 ng/mL, Biolegends). Treated organoids were dissociated and subjected to scRNA-seq using both methods.
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3

Macrophage Differentiation and Activation

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Recombinant human macrophage colony-stimulating factor (M-CSF), receptor activator of NF-κB ligand (RANKL) and mouse RANKL were purchased from BioLegend (San Diego, CA, United States). Tunicamycin was obtained from Cayman Chemical Co. (Ann Arbor, MI, United States).
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4

Osteoclast Differentiation from Murine Bone Marrow

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To obtain osteoclast precursor cells, bone marrow mononuclear cells (BMMCs) were collected from tibias and femurs of C57BL/6 mice and were cultured in the wells of a 96-well plate (3.0 × 105 cells/well) or 24-well plate (1.0 × 106 cells/well) with a minimum essential medium-α (MEM-α) supplemented with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin and 100 U/mL penicillin as well as 292 μg/mL L-glutamine and 50 ng/mL M-CSF (BioLegend) at 37 °C in humidified air with 5% CO2 for 3 days. Subsequently, the OC precursors were differentiated to osteoclasts using 50 ng/mL RANKL (BioLegend, San Diego, CA, USA).
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5

Osteoclast Differentiation Assay of Aged Mice

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Mononuclear bone marrow cells isolated from femur and tibia of aged wild type mice (twenty four month old) were seeded in 96-well plates at a density of 1 × 105 cells/well in α-MEM medium (Life Technologies) containing 10% FBS (Atlanta Biologicals) and 20 ng/ml of MCSF and 10 ng/ml of RANKL (BioLegend) recombinant proteins in the presence or absence of polymethylmethacrylate (PMMA) particles (mean diameter 6.5 μm; Bangs Laboratories), mouse MIF recombinant protein (R&D), and Glycyrrhizin (Tokyo Chemical Ind.) as described in earlier studies [12 (link),33 (link),36 ,37 (link)] Five days later, cells were stained for tartrate-resistant acid phosphatase (TRAP) using a leukocyte acid phosphatase kit (Sigma). TRAP positive (TRAP+) cells with more than three nuclei were considered mature osteoclasts and were microscopically counted. The results were expressed as numbers per well.
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6

Osteoclastogenesis from Murine Bone Marrow

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Bone marrow was collected from femurs and tibias of 8-week-old, male C3H/He mice (Japan SLC) and cultured for 3 days at a density of 5 × 106 cells/100-mm dish in MEMα (FUJIFILM Wako, Osaka, Japan) supplemented with 10% FBS and 100 ng/mL of macrophage colony-stimulating factor (M-CSF; BioLegend, San Diego, CA, USA). To induce osteoclast precursor cells (OPCs), the cells were cultured for additional 3 days at 5 × 105 cells/100-mm dish. For osteoclastogenesis, OPCs were cultured for 5 days at 1 × 105 cells/12-well plate in MEMα with 10% FBS, 20 ng/mL M-CSF, and 50 ng/mL of receptor activator of NF-kappaB ligand (RANKL; Biolegend). To determine effects of SEVs, 1 × 1010 particles/mL or indicated doses of SEVs were added to the medium at the beginning of osteoclastogenesis. To determine the effects of miRNA, 60 pmol of miRNA mimic transfection control with Dy547 (miR-Ctrl) or hsa-miR-146a-5p mimic (Horizon Discovery, Cambridgeshire, United Kingdom) was transfected into OPCs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) at the beginning of osteoclastogenesis. Cellular growth was evaluated using WST-8 assay reagent (Nacalai Tesque, Kyoto, Japan). TRAP staining was performed after 5 days of osteoclastogenesis by using an Acid Phosphatase Leukocyte Kit (Merck), and was evaluated using microscopy BZ-X710 and BZ-X Analyzer.
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7

Osteoclastogenesis Assay with RAW 264.7 Cells

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Osteoclastogenesis assay was performed with RAW 264.7 cells (1.5*104 cells per well in a 24-well plate) that were incubated with 30 ng/ml RANKL (Peprotech, Israel) for 5 days. RANKL-treated cells were also treated with Zol and/or Dex, recombinant mouse IFN-β (0.25 or 2.5 ng/ml, Biolegend), or anti-IFN-β antibodies (2 μg/ml, Abcam, United Kingdom) for the first 2 days of incubation and then washed. RANKL was supplemented after washing.
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8

Osteoclast Differentiation Assay of Aged Mice

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Mononuclear bone marrow cells isolated from femur and tibia of aged wild type mice (twenty four month old) were seeded in 96-well plates at a density of 1 × 105 cells/well in α-MEM medium (Life Technologies) containing 10% FBS (Atlanta Biologicals) and 20 ng/ml of MCSF and 10 ng/ml of RANKL (BioLegend) recombinant proteins in the presence or absence of polymethylmethacrylate (PMMA) particles (mean diameter 6.5 μm; Bangs Laboratories), mouse MIF recombinant protein (R&D), and Glycyrrhizin (Tokyo Chemical Ind.) as described in earlier studies [12 (link),33 (link),36 ,37 (link)] Five days later, cells were stained for tartrate-resistant acid phosphatase (TRAP) using a leukocyte acid phosphatase kit (Sigma). TRAP positive (TRAP+) cells with more than three nuclei were considered mature osteoclasts and were microscopically counted. The results were expressed as numbers per well.
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9

Murine Intestinal Crypt Isolation and Organoid Culture

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Murine small intestinal crypts were isolated and cultured as previously described (De Lau et al., 2012 (link); Sato et al., 2009 (link)). Briefly, ileums were flushed, opened longitudinally and cut into 2–4 mm segments. Tissues were incubated in 2 mM EDTA / PBS for 30 min on ice, pipetted, then washed to release crypts into the supernatant. Supernatant was passed through a 70 um strainer and centrifuged at 300 g for 5 min. Crypts were grown in Matrigel (Corning) in 24-well plates with Advanced DMEM / F12 cell culture media (Life Technologies) supplemented with growth factors including EGF (50 ng/ml, Life Technologies), Noggin (100 ng/ml, PeproTech), and R-spondin-1 conditioned media (supplied by Harvard Digestive Diseases Center Gastrointestinal Organoid Culture Core). For stimulation of organoids, RANKL (200 ng/ml, Biolegend) was added to wells either alone or with CGRP (1, 10, 100 nM, GenScript) and incubated for 72 hr. Fresh media, RANKL, and CGRP was replaced at 48 hr. To harvest cells, organoids were placed in Cell Recovery Solution (Corning) for 30 min prior to washing and resuspending in Trizol, then stored at −80°C prior to RNA extraction.
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10

Osteoclast Differentiation from PBMCs

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Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density gradient centrifugation (density: 1.077 g/mL; PanBiotech, Aidenbach, Germany) and washed twice with DPBS (Gibco).
Cells were then resuspended in alphaMEM Glutamax (Gibco, Life technologies, Darmstadt, Germany) supplemented with 10% FCS, 100 U/mL penicillin (Life technologies, Darmstadt, Germany), 10 μg/mL streptomycin (Life technologies), and 25 ng/mL MCSF (BioLegend, Amsterdam The Netherlands). The cells were seeded at specific concentrations, depending on the culture plate used (1.5 × 106 cells/well in 6 well plates, 0.15 × 106 cells/well in 48 well plates, and 0.05 × 106 cells/well in 96 well plates) and cultured at 37 °C, 5% CO2. After 24 h, the medium was replaced with a differentiation medium containing alphaMEM Glutamax (Gibco, Life technologies, Darmstadt, Germany) supplemented with 10% FCS, 100 U/mL penicillin (Life technologies), 10 μg/mL streptomycin (Life technologies, Darmstadt, Germany), 25 ng/mL MCSF, and 50 ng/mL RANKL (BioLegend, Amsterdam The Netherlands). As an osteoclast differentiation control, cells were cultured without RANKL. The cells were cultured for 14 days, and the medium was replaced twice a week.
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