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9 protocols using facs symphony a3

1

Quantifying Cellular Oxidative Stress

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For ROS measurements, cells were incubated for 30 min at 37 °C with 2 μM of dichlorodihydrofluorescein diacetate (DCFDA, Molecular Probes). Cells were collected using Trypsin, washed twice with PBS, and resuspended in 250 µL of FACS buffer (PBS, 1% BSA, 0.05 sodium azide). Measurements were made using BD FACS Symphony A3 and the acquired data were analyzed using FlowJO software.
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2

Flow Cytometric Analysis of Adipose B Cells

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Isolated cells were incubated with Ghost Dye Red 780 Viability Dye (TONBO biosciences) for 30 minutes on ice, in the dark, then washed and stained with FcBlock and surface antibodies for 45 minutes to 12 hours at 4°C in the dark. Antibodies used are documented in Table S1. For intracellular staining of cytokines, cells were treated with GolgiStop (containing monensin) for 4 hours and fixed for 20 minutes using fixation/permeabilization solution (BD, 554715) prior to intracellular staining for 45 minutes. Analysis was performed on a BD Fortessa X-30 and BD FACSSymphony A3 cytometers and using FlowJo v10; gating schemes are shown in relevant supplementary figures. Antibodies used can be found in Table S1. For fluorescence associated cell sorting: 15,000 live CD45+ CD19+ CD11b+ and live CD45+ CD19+ CD11b were sorted on a BD FACS Aria II into RPMI with 40% FBS. Cells were pelleted and resuspended in RNA lysis buffer (Invitrogen; 46-6001) for RNA isolation. Adipose B cells were pooled from 2 mice per sample to account for biological variability.
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3

Cell Proliferation Analysis on NIR-Irradiated Scaffolds

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WST-1(4-(3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio)-1,3-benzene-disulfonate (ROCHE/CELLPRO-RO) colorimetric assay was carried out to determine the effects of NIR laser irradiation (808 nm) on cell proliferation at the above indicated condition. The assay was performed by 48-well plates, with seeding of 4T1 (5 × 103 cells/well), A549 (1 × 104 cells/well), RAW264.7 (3 × 104 cells/well) cells on PLGA, PLGA-GO1% and PLGA-GO2% scaffolds. After each NIR application, cells were cultured for additional 24 h s and 30 μL per well of WST-1 solution were added to the culture medium and incubated for 2 h at 37 °C and 5% CO2. Absorbance was subsequently determined using Cytation 3 Cell Imaging Multi-Mode Reader (Biotek) applying the wavelengths 450 nm for measurements and 650 nm for reference. All experiments were conducted in two wells for each condition and replicated at least three times. Cell proliferation was calculated by comparing the absorbance values of the samples after background subtraction. Cell viability was expressed as the percentage of cells seeded on PLGA. Cell viability of human PBMCs was assessed by staining PBMC harvested from the different culture conditions and by staining cells with E-Fluor 780 (Thermofisher) to exclude dead cells. Stained cells were then acquired at FACS Symphony A3 within 1 h and results analyzed using Flowjo 10.7v (BD Biosciences).
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4

Cell Cycle Analysis by Flow Cytometry

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Single cell suspensions were generated as described above. Cells were stained extracellularly with CD31 and live/dead stain as described above. Thereafter, cells were fixed and permeabilized with 70% EtOH overnight. Cells were washed twice with MACS buffer and subsequently stained with propidium iodide (PI, Molecular Probes,) staining solution (20 µg/ml PI, 200 µg/ml RNase A in PBS, Molecular Probes, #F10797) for 30 min at RT. Cells were diluted in PBS and analyzed at a FACS Symphony A3 (BD) flow cytometer. The PI signal was detected in the PE channel. Cell cycle analysis was performed using FlowJo 10.9.0 using “Cell Cycle” function and a pragmatic Watson model.
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5

Characterization of T Cell Subsets

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T helper (Th1, Th2, and Th17) and Treg subpopulations were identified by flow cytometry analysis for the expression of specific cell surface markers and transcription factors. After being co-cultured for 5 days with or without PLGA scaffold alone or with GO (0.5, 1, 2, 5%), activated PBMCs were harvested and centrifuged at 300 g for 5 min. The viable dye E-Fluor 780 from Thermofisher was used to eliminate dead cells. CD3 (clone UCHT1), CD4 (clone VIT-4), CD45RA (clone HI100), CD196 (clone 11A9), CD183 (clone 1C6/CXCR3), CD25 (clone M-A25) all purchased from BD biosciences and CD194 (clone REA279) from Miltenyi. After fixation and permeabilization with BD Cytofix/Cytoperm (BD Biosciences), intracellular staining for the transcription factor FoxP3 was carried out by incubating cells with anti-FoxP3 antibody (clone R16-715, BD Biosciences) 4 °C for 30 min in the dark. FACS Symphony A3 (BD Biosciences) was used to acquire the samples, and Flowjo 10.7v (BD Biosciences) was used to analyze the results. Th subsets and Treg were identified by the following gating strategy: first, CD4+CD45RA negative cells were gated to identify T effector cells, then Th subsets were identified as follows: Th1 as CD196-CD183+, Th17/Th1 as CD196+CD183+, Th2 as CD196-CD183-CD194+, and Treg as CD25hiFoxP3+ [37 (link)].
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6

Evaluating Stemness Markers in Cancer Cells

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The proportion of CD44 and CD133 positive cells in SNU478 cells was measured by FACS analysis. After 48 h of cordycepin (20 μM) and/or gemcitabine (500 nM) treatment, cells were harvested. After washing, cells were reacted with FITC-conjugated anti-human CD44 (Clone BJ18; BioLegend) and APC-conjugated anti-human CD133 (Clone clone7; BioLegend) antibody. Stained samples were detected by FACS Symphony A3 (BD Bioscience) and results were analyzed by the FlowJo Software v. 10.8.1 (TreeStar).
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7

Multiparameter Analysis of BM Cell Subsets

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BM cells prepared above were stained with lineage markers on FITC (CD4, CD5, CD8, CD11b, B220, Gr1, Ter119, and CD41, eBioscience, San Diego, CA, USA), CD117-APC-H7 (BD Bioscience, San Jose, CA, USA), Sca1-PE (eBioscience), CD16/32-PerCP5.5 (BD Bioscience), CD150-PE-Cy7 (BioLegend, San Diego, CA, USA), and CD105-BV421 (BD Bioscience) for 30 min on ice and gating as described by Pronk et al (34 (link)). and Singer et al. (12 (link)). Dead cells were excluded using 7-Amino-Actinomycin D (7-AAD; eBioscience) and AccuCheck counting beads (PCB100, Invitrogen) were used for quantification of absolute cell numbers. Multiparameter analysis was performed on a FACSSymphony A3 (BD Bioscience) using the FACSDiva software and data were analyzed using the FlowJo software (version 10, Tree Star Inc., Ashland, OR, USA).
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8

Multiparameter Analysis of Immune Cell Subsets

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Blood was collected from tail veins in the presence of 5 mM EDTA, incubated with BD Fc Block for 10 min, and then stained with mAbs (BD Bioscience unless indicated otherwise) specific to CD45-APC-Cy7 (clone 30-F11), Ly6G-eFluor450 (1A8-Ly6g, eBioscience), CD11b-PerCP-Cy5.5 (M1/70), Ly6C-FITC (AL-21), NK1.1-APC (PK136), CD3-APC (145-2C11), CD19-APC (1D3), and TER119-APC (TER-119, eBioscience) for 20 min at room temperature. The samples were then fixed and lysed using BD FACS Lysing solution (BD Bioscience). After fixation, cells were washed and resuspended in 2% FBS/PBS. AccuCheck counting beads (PCB100, Invitrogen, Grand Island, NY, USA) were used for quantification of absolute cell numbers. Multiparameter analysis was performed on a FACSSymphony A3 (BD Bioscience) using the FACSDiva software and data were analyzed using the FlowJo software (version 10, Tree Star Inc., Ashland, OR, USA) as described previously [10 (link)].
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9

CTLA-4-Mediated Competition Assay

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HEK293-F cells transiently expressing surface CTLA-4 were transfected as previously described 24 to 48 h prior to incubations. HEK293-F cells (either stably or transiently expressing surface CTLA-4) were incubated with titrations of proteins for 2 h at 37 °C and with a constant concentration of B7.1-Fc for 1 additional hour for the competition assays. Cells were stained for viability, washed with PBSA, and analyzed with a FACS Symphony A3 (BD). Additional details are provided in SI Appendix.
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