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9 protocols using helix np nir

1

NK Cell-Mediated Cytotoxicity Assay

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Target YAC‐1 cells were labelled with carboxyfluorescein succinimidyl ester (CFSE; C1031, Beyotime) at a final concentration of 5 μM. They were then co‐cultured with effector NK cells at an effector‐to‐target cell (E:T) ratio of 2:1 or 0:1 for 4 h at 37°C under 5% CO2. After 4 h, the samples were stained with Helix NP NIR (425301, BioLegend) and Annexin V‐PE (640908, BioLegend) for 10 min. Fluorescence‐activated cell sorting (FACS) analysis was performed immediately with a BD LSR Fortessa Cell Analyzer (BD Biosciences). The Incucyte S3 Live‐Cell Analysis Instrument (Sartorius AG) was used to monitor the killing activity of NK cells. Propidium iodide (C1052, Beyotime) was used to mark dead cells.
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2

Measurement of Cellular Oxidative Stress

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ROS production was measured by flow cytometry using dihydrorhodamine 123 (DHR123). Cells were preincubated for 20 minutes at 37 °C. The indicated agonists and DHR (2 µM) were then added for 15 minutes. To stop the reaction, cells were placed on ice, washed, and resuspended in Cell Wash (BD Bioscience) containing 0.5% PFA and 50 nM of the cell-impermeant far-red emitting nucleic acid stain Helix NP NIR (Biolegend) to gate for live cells. 10,000 live cells per condition were analysed on a Guava easyCyte™ System (Millipore, Burlington, MA, USA) for median fluorescence intensity. Agonist-mediated ROS production was expressed as percentage of the signal detected in untreated cells. The FPR2/ALX specific agonist WKYMVm was used as a positive control.
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3

hNPC NSC-6 Antigen Immunophenotyping

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Plated human iPSC-derived NPCs (hNPCs) were harvested using Accutase cell dissociation solution (GIBCO), washed in ice-cold flow buffer (DPBS, 2% fetal bovine serum, 2 mM EDTA). In each condition, 1 × 106 cells were incubated with the NSC-6 antibody for 45 min on ice (1:20; optimal concentration determined by previous titration experiments). The cells were then washed twice in ice-cold flow buffer with 2% normal donkey serum added, then stained in the same buffer with Alexa Fluor 405 (1:200 donkey anti-mouse IgG H&L; ABCAM 175659) secondary antibody for 45 min on ice. Stained cells were washed twice in ice-cold flow buffer then resuspended in a viability dye solution (20 mM Helix NP NIR, BIOLEGEND, 425301 in flow buffer) and immediately analyzed by flow cytometry using an LSR Fortessa (BECTON DICKINSON) with acquisition of AF405 on V450 and Helix-NIR on R670. Final data analyses were performed using FlowJo software (TREE STAR INC.). To determine hNPC NSC-6 positivity, 250,000 live cell events were acquired. NSC-6 positive signal was set by gating for single viable cells and above background, the latter determined using the signals obtained from unstained hNPCs and hNPCs stained with the secondary antibody only.
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4

NET Induction in Human Neutrophils

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BM Neutrophils (> 95% purity) were resuspended in RPMI medium containing 10% FCS (1 x 106/ml) and incubated for 37°C and 5% CO2 for 30 min. To induce NETosis, the cells were exposed to the activating agent PMA (10, 30 nM; Sigma-Aldrich) or fMLP (100, 1000 nM; Sigma-Aldrich) for 0-4 hrs at 37°C. NET induction was terminated by 4% PFA for 15 min. Helix NP™ NIR (0.1 µM; Biolegend) and DAPI (0.3 nM; Biolegend) were added to detect NETs. Data acquisition (Helix NP™ NIR+ DAPI+ Cells) was done on FACSCelesta SORP (BD) flow cytometer and analyzed with FlowJo software (Treestar).
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5

Assessing Cellular Unfolded Protein Load

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Following treatment with SpiD3 or thapsigargin, CLL cell lines (1e6 cells/mL; 4 hours) or CpG-stimulated patient-derived CLL samples (1e7 cells/mL; 24 hours) were stained for 30 minutes with 50 µmol/L thiol probe, tetraphenylethene maleimide (TPE-NMI), to assess cellular levels of SEC residues (unfolded/misfolded protein load; ref. 27 (link)). Helix NP NIR (BioLegend) was added for live/dead discrimination prior to flow cytometry analysis. Fold change in MFI was calculated as treatment group MFI/control MFI.
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6

Multiparametric Flow Cytometry for Tissue Composition

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To analyse the cellular composition in different tissues, cell staining was performed for 30 min at 4℃ in the dark with fluorescent mAbs as described previously.22 Before staining, cells were washed with staining buffer containing 0.1% BSA and 0.05% sodium azide and blocked with CD16/32 Ab for 15 min on ice to reduce non‐specific binding. For surface molecular detection, the following mAbs were used (all from BD Biosciences, Thermo Fisher Scientific and Biolegend): CD45‐FITC/PE (30‐F11), CD19‐PerCp‐Cy5.5/PE‐Cy7 (1D3), CD3‐PE‐CF594 (145‐2C11); CD103‐PE/PE‐Cy7 (2E7), CD69‐PE/PE‐Cy7 (H1.2F3), CD62L‐APC (MEL‐14), CD138‐PE (281‐2), IgM‐APC‐Cy7 (II/41), IgM‐PECF594 (R6‐60.2), IgD‐APC (11‐26c, 2a), IgG‐FITC (Poly4060), IgG‐PE‐Cy7 (Poly4053), IgA‐PE (mA‐6E1), IgA‐FITC (C10‐3 ), CD23‐PE (B3B4), CXCR3‐PE (CXCR3‐173), CXCR5‐PE‐Cy7 (2G8), CX3CR1‐PE (SA011F11), CCR5‐PE (HM‐CCR5), CD80‐PE (16‐10A1), CD24a‐FITC (M1/69), CD38‐FITC/PerCp‐Cy5.5 (90). Dead cells were excluded by Helix NP™NIR (Biolegend) staining. Cell samples were performed on FACS Aria II (BD Biosciences), and data were analysed by FlowJo10 (TreeStar, San Carlos, CA, USA).
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7

Cell Membrane Integrity Assay

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Cells were treated with the indicated agonists for 15 minutes at 37 °C and were then washed and resuspended in Cell Wash (BD Bioscience) containing 50 nM of the cell-impermeant far-red emitting nucleic acid stain Helix NP NIR (Biolegend, San Diego, CA, USA) for detection of compromised cells. A Guava easyCyte™ System (Millipore, Burlington, MA, USA) was used to determine the percentage of Helix NP NIR-negative cells per 10,000 cells analysed. Triton X-100 (1%) was used as a positive control.
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8

Cell Proliferation and Viability Assay

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Cells were stained using the CellTrace Violet Cell Proliferation Kit (Invitrogen, # C34557) according to manufacturers protocol. 30,000 cells were then seeded in 24‐well plates and treated as described in each figure. After the treatment period, cells were detached using trypsin and collected by spinning at 1800 x rpm for 5 min. Cells were washed in 1 x PBS and transferred to flow cytometry tubes. Cells were then stained with Helix NP NIR (BioLegend) for live/dead cell sorting, according to manufacturer's protocol. Flow cytometry data was acquired on a BD LSRFortessa by the Flow Cytometry core at Georgetown University Medical Center. Results were analysed using FlowJo (BD Biosciences).
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9

Multiparameter Flow Cytometry of GFP, DiI, and CellTrace Violet Labeled Cells

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DiI and CellTrace Violet (Thermo Fisher C34571) labeled GFP-expressing MDA-MB-231 cells were seeded into four Nunc™ polystyrene cell culture flasks. Each day one flask was washed with PBS, harvested, and analyzed on a BD Fortessa SORP (Becton Dickinson, San Jose CA). Dead cells were excluded from the analysis utilizing Helix NP NIR (Biolegend 425,301). 30000 cells were collected for each sample. Fluorescence signals from the 488 nm laser line excitation were analyzed to detect the GFP and DiI emission at 530 nm and 575 nm respectively, fluorescence signals from 640 nm excitation were analyzed to detect the Helix NIR emission at 660 nm and fluorescence signals from 405 nm excitation were analyzed to detect the CellTrace Violet emission at 450 nm. Autofluorescence of DiI unlabeled cells or wild-type MDA-MB-231 cells that were not genetically modified to express GFP were used as negative controls. The cutoff fluorescence intensity was set so that 99.9% of the control cell autofluorescence. The percentage of positive cells was determined as the percentage of cells that exceeded the cutoff for each of the three parameters (GFP, DiI or CellTrace labeling). Results were analyzed utilizing FCS Express 7 software (DeNovo Software, Pasadena CA).
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