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13 protocols using mab004

1

NK Cell Activation via NKR Ligands

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Receptor agonists were adsorbed onto tissue culture plates for 24 hours prior to NK cell harvesting and plating. A total of 300 μL of the following PBS solutions were added to 24-well plates and incubated at 4°C overnight: anti-NKp46 (5 μg/mL; [R&D Systems; catalog MAB1850]), recombinant MICA Fc-chimera (1.25 μg/mL [R&D Systems; catalog 1300-MA]), recombinant MICB Fc-chimera (1.25 μg/mL [R&D Systems; catalog 1599-MB]), and isotype (20 μg/mL IgG2b; [R&D Systems catalog MAB004]); anti-NKp46 (5 μg/mL; [R&D Systems catalog MAB1850]), recombinant MICA Fc-chimera (1.25 μg/mL [R&D Systems; catalog 1300-MA]), recombinant MICB Fc-chimera (1.25 μg/mL [R&D Systems; catalog 1599-MB]), and anti-NKG2A (20 μg/mL; [Beckman Coulter catalog IM2750]); or isotype only (25 μg/mL IgG2b [R&D Systems catalog MAB004]). After 24 hours, plates were washed twice with PBS and NK cells were added; NK cells were counted and resuspended in B0 medium supplemented with 1 ng/mL IL-15 (R&D Systems) at a density of 1 × 106 cells/mL. NK cells were added (1 × 106 cells/well) to each well of the previously prepared 24-well plates. After 7 days (including replating at day 3 as described previously) NK cells were harvested, washed with PBS, counted, and used for various experiments.
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2

Influenza Infection in A549 Cells

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A549 cells were seeded onto 6-well plates and transfected with siRPS16 (or siNC control). After 48h of transfection, the cell was infected with influenza A/WSN/1933 (MOI = 0.1), the cells were maintained with medium containing IFN-β neutralizing antibody (2 µg/ml) (R&D system, MAB8141) or same concentration of antibody iso-type control IgG (R&D system, MAB004). The NP protein expression was tested by western blot assay at 24 h post infection.
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3

Transwell Migration Assay for BMSC and MB Cells

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Migration assays were carried out in a 24-well transwell system equipped with porous (8 μm) polycarbonate membranes. 2 × 105 MB cells were resuspended in 600 μL of growth medium supplemented with 1% FBS and plated into the lower chamber of the transwell system; 5.0 × 104 BMSC cells were resuspended in 200 mkl of growth medium supplemented with 1% FBS and plated into Transwell inserts which were then placed into another transwell system with the lower chamber filled with 600 μl of serum-free medium. After 24 hours the cells on the inserts or in lower chambers were transfected as indicated, 6 hours after the transfection the media was changed and the inserts with BMSC, were placed into the wells with MB cells and incubated at 37 °C for 24 h. When indicated, CXCR4 (Abcam, #ab10403) or SDF1 (CXCL12) (Abcam, #ab9797) antibodies were added to the medium at 10 mkg/ml and 4 mkg/ml concentrations respectively. The inserts were then discarded, and upper sides of the filters were swabbed to remove the cells that did not cross the membrane. The cells present on the lower side of the filters were then fixed in 4 % paraformaldehyde, stained with DAPI and the counted under the microscope. All the experiments were performed in duplicate. The following control antibodies were used: rabbit IgG control (AB-105-C, R&D systems) and mouse IgG2b isotype control (MAB004, R&D systems).
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4

Maternal Anti-BMP Antibody Effects on Neonatal Retinal Development

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Lactating dams were injected i.p. once on P3 with PBS, mouse monoclonal isotype control Abs (15 mg/kg, IgG2b, MAB004; 15 mg/kg, IgG2a, MAB003; R&D Systems), or mouse monoclonal anti-BMP9 and anti-BMP10 Abs (15 mg/kg, IgG2b, MAB3209; 15 mg/kg, IgG2a, MAB2926; R&D Systems, respectively). As controls, groups of neonates were directly injected i.p. on P3 with PBS or the same mouse monoclonal isotype control or anti-BMP9 and anti-BMP10 Abs (15 mg/kg). Neonates were euthanized by CO2 asphyxiation on P6 and non-heparinized blood was collected. Neonates were enucleated and eyes fixed in 4% paraformaldehyde for 20 min on ice and retinas were isolated.
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5

Evaluating IL-25 and IL-13 Antibodies in Gastric Tumors

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13-week-old gp130F/F mice were given 1x weekly injection for 3 weeks of either α-IL25 (R&D Systems, MAB13992), α-IL13 (R&D Systems, MAB413) or IgG control (R&D Systems, MAB006 and MAB004) (at 300 μg/mouse). 1 week after the last injection, mice were euthanized via CO2 asphyxiation. Stomachs were collected and tumors were excised and weighed before being fixed in 10% NBF overnight at room temperature.
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6

Transwell Assay for T Cell Barrier Function

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After enrichment, CD3+ T cells were counted, and half of the cells (UTC) was plated in 600ul HI medium at the basolateral side of the transwell insert (1∗105 cells per transwell). The other half of T cells was activated (STC) to produce cytokines by 2 h incubation with phorbol 12-myristate 13- acetate 50 ng/ml (PMA, Santa Cruz/Bio-Connect, cat#sc-3576A) Ionomycin 1000 ng/ml (IONO, Invitrogen, cat#I-24222) at 37°C. Subsequently, cells were counted again and plated in 600ul HI medium at the basolateral side of the transwell insert (1∗105 cells per transwell). One well was cultured in the absence of T cells in HI medium serving as the control condition. After 72 h co-culture TEER was measured. To validate the effect of IFNγ inhibition on TEER, we performed the same experiment as above by adding IFNγ antibody inhibitor 10μg/ml (R&D, #MAB2851-100) or Mouse IgG2B Isotype Control (R&D, # MAB004, Clone 20116) to each transwell condition for 72 h before TEER measurement.
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7

Isolating and Studying Differentiated Ductal-like Cancer Cells

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Organoid-derived CD44(-)PI(-) differentiated ductal-like cancer cells were sorted using flow cytometry (FACS Aria III). Then, we established them with CFSE-labeled endothelial cells in round-bottom ultra-low attachment plates (Corning) and cultured them with 10 μg/ml of JAG1-neutralizing antibody (R&D Systems, MAB12771) and control mouse IgG2b (R&D Systems, MAB004). After 1 day, the assembloids were washed and then embedded in GFR Matrigel and cultured in the basal medium containing JAG1-neutralizing antibody or mouse IgG2b. After 6 days, the assembloids were subjected to a FACS analysis to determine the CIC population.
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8

Chromatin Immunoprecipitation (ChIP) Assay

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ChIP assays were performed as previously described (46 (link)). Briefly, aliquots of 2.5×106 formaldehyde-fixed cells were resuspended in 50 μl nuclei isolation buffer (Abcam, Cambridge, United Kingdom), and chromatin was digested with 15 U MNase (ThermoFisher) for 5 min. at 37ºC. EDTA was added to stop the reaction. After enzymatic digestion, antibodies against Runx1 (ab23980, Abcam), Runx2 (AF2006, R&D Systems, Minneapolis, MN), Runx3 (353604, BioLegend), TET2 (PA5–35847, ThermoFisher), and TET3 (PA5–34431, ThermoFisher) were added to precipitate the sheared chromatin. An IgG isotype antibody (MAB004, R&D Systems) was also added for a background control. After washing steps, protein and DNA complexes were eluted and cross-links were reversed. Purified DNA samples were analyzed by quantitative real time PCR with primers listed in Supp. Table 1.
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9

Neutrophil Migration Assay with Conditioned Media

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Neutrophil isolation was performed as previously described (Albrengues et al., 2018 (link)). Transwell migration assays were performed with conditioned media derived from cell lines ectopically expressing p63 or the empty vector that were cultured alone or in combination with mouse PSCs for five days in Matrigel. 5 × 103 SUIT2 cells and 4 × 104 PSCs were used for the co-cultures. The conditioned media were added to the lower chamber, and primary mouse neutrophils (2.5 × 105) were seeded in 0.5% FBS containing DMEM in the upper chamber of a 3 µm FluoroBlok cell culture insert (08-772-141; Corning) in a 24 well plate. 500 ng of recombinant mouse (250-11; Peprotech) or human (300-11; Peprotech) CXCL1 was added to DMEM with 5% FBS on the day of seeding neutrophils as controls. For experiments with blocking antibodies, 10 μg/ml human CXCL1 (MAB275-100; R and D Systems) or IgG2B isotype control (MAB004; R and D Systems) was added to the neutrophils prior to the addition of the conditioned media. After 24 hr, the FluoroBlok membrane was stained with DAPI (0.05 mg/ml; D1306; Thermo Fisher Scientific) for 5 min, rinsed in water and mounted onto glass slides using mounting media (17985–16; Electron Microscopy Sciences). The number of invading neutrophils was counted in 10 random fields of view using a fluorescence microscope (Leica SP8 Confocal microscope).
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10

Organoid cytokine response assay

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Two days after seeding into Matrigel, organoids were grown in the presence of either IL25 (R&D Systems, 1399-IL), IL13 (R&D Systems, 413-ML), α-IL25 (R&D Systems, MAB13992), α-IL13 (R&D Systems, MAB413) or either PBS or IgG control (R&D Systems, MAB006 and MAB004) antibodies (at 20 ng/ml). Media and antibodies were replaced every second day.
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