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205 protocols using facsvantage

1

Isolation and Purification of T Cell Subsets

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Splenic CD4+ or CD8+ T cells were isolated by negative selection from single-cell suspensions of SPLs using a CD4+ T cell isolation kit II or a CD8+ T cell isolation kit II (Miltenyi Biotec). To get naïve CD4+ or CD8+ T cells, purified CD4+ or CD8+ splenic cells were stained with fluorescence-labeled antibodies against CD44 and CD62L. Then CD44lowCD62Lhigh subsets were sorted using a FACSVantage (BD Biosciences). To purify thymic double negative (DN), double positive (DP), CD4 single positive (SP), and CD8 SP cells, single-cell suspensions of thymi were stained with fluorescence-conjugated antibodies against cell surface markers CD4 and CD8; different subsets were then sorted using a FACSVantage (BD Biosciences). In each case, purity of the cell separation was verified by flow cytometry analysis. Cell purity was verified to be at least 95%.
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2

Quantifying Side Population Cells in HCC

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To examine the percentage of side population (SP) cells, HCC cells with or without 24 h inflamed-CM treatment were sorted through FACS flow cytometry (FACS Vantage, Becton Dickinson, San Jose, CA, USA). In brief, HCC cells were trypsinized and incubated at 4°C for 30 min with Hoechst red and Hoechst blue (Cell Signaling Technology, Danvers, MA). The nonspecific fluorescence signals were excluded using an antiporter-specific inhibitor, FIC. Labeled cells were analyzed and separated using a cell sorter (FACS Vantage, Becton Dickinson). The percentage of SP cells was determined by subtracting the percentage of parent (H + FTC) from the percentage of parent (H) {(% of SP = % of parent (H) − % of parent (H + FTC))}. Collected data were analyzed using CELLQuest software (Becton-Dickinson Immunocytometry Systems, San Jose, CA, USA). Gating was implemented based on negative-control staining profiles. SP cells were seeded in culture dishes for additional experiments.
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3

Fibroblast-Tumor Cell Co-culture Transcriptome Analysis

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Co-cultures were started by plating 0,5 × 106 fibroblasts in collagen coated 10 cm dishes for 5–7 days. When cells reached full-confluency and the monolayers were matured, cells were washed 3× with PBS and 0,5 × 106 PC-3 mRFP tumor cells were added for 4 days in complete medium. After 4 days of co-culture, the cells were washed 3× with PBS, trypsinized, and then the fibroblasts were sorted using BD FACSVantage (CA, USA). Total RNA was purified from flow cytometry sorted fibroblasts with and without PC-3 mRFP confrontation using the RNA Purification Kit (Ambion, USA) according to the manufacturer’s instructions. The Affymetrix Gene Chip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for preparation of cDNA from 150 ng of total RNA. Array hybridization, washing, staining and scanning were performed on the Gene Titan system using the Gene Chip Human Gene 1.1 ST Array plate. Combining the probes, normalization and background correction were performed in Affymetrix Expression Console (v. 1.3.1) using the RMA method.
The data are available at Gene Expression Omnibus under Accession number GSE57199: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57199.
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4

Flow Cytometric Detection of CD11b

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For detection of the cell differentiation antigen, CD11b, ATRA (Sigma-Aldrich; Merck Millipore) was used to induce cell differentiation at a concentration of 1 nM for 3 days. The cells (1×106/group) were washed twice with PBS and incubated with phycoerythrin (PE)-conjugated CD11b antibody (cat. no. 12-0113-42; eBioscience, Inc., San Diego, CA, USA) at 4°C for 30 min in the dark. The cells were then analyzed using flow cytometry (BD FACS Vantage; BD Biosciences, San Jose, CA, USA) and CellQuest Pro software version 5.1 (BD Pharmingen, San Diego, CA, USA).
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5

Cell Cycle and Apoptosis Analysis of U251MG

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The U251MG cells were plated in six-well plates. When cell confluence reached 80%, the liposomes and free curcumin were respectively added into the media at a final concentration of 20 μM. After another 48 h incubation, the cells were collected with 0.25% trypsin/EDTA and centrifuged at 1,000 rpm for 5 min, and then fixed in 70% ethanol for 24 h. Afterwards, cell cycle (propidium cell cycle assay kit; Beyotime Inst. Biotech., Shanghai, People’s Republic of China) was measured using a flow cytometer (BD FACSVantage; San Jose, CA, USA). Moreover, after the cells were treated with RCL (final concentration, 20 μM), cell apoptosis (Annexin V-PE apoptosis detection kit; Beyotime Inst. Biotech.) was measured by flow cytometry.
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6

Intracellular Calcium Flux Monitoring in T Cells

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CD8CD44lo OT-1 T cells (5 × 106 cells) were loaded with 1.8 µM Indo-1 (ThermoFisher Scientific, Cat. No. 1223) in Indo buffer (HBSS with calcium and 0.5% BSA) at 37 °C for 30 min. The cells were washed twice with the buffer and let stand for 40 min at 4 °C with a gentle shaking at 20 min, followed by washing twice in Indo buffer. The cells resuspended in the buffer (0.5 mL) were heated to 37 °C for 2 min, added with DCs (5 × 106 cells in 0.5 mL), and spun using a minifuge for 20 s to have the T cells contact with DCs, without IL-2. Various times later (1 to 8 min), the cell mixture was resuspended by a short vortexing and applied to a flow cytometer (BD FACSVantage, BD Bioscience). The 405/510 nm emission signal ratio for Indo-1 (Indo-1 ratio) was used to analyze the intracellular Ca2+ flux. The peak of median of the top 60% Indo-1 ratios for each of the samples incubated for different times was plotted against the duration of DC-T cell contact to obtain intracellular Ca2+ concentration changes induced by the contact with DCs. In some experiments, DCs loaded with ovalbumin peptide (SIINFEKL, American Peptide Company/Bachem) were used to induce TCR stimulation-mediated Ca2+ flux as a control.
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7

Lentiviral Transduction and Enrichment

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JygMC(A) cells were transduced with a lentivirus vector containing a fusion construct of the firefly luciferase and eGFP reporters (Leidos/FNLCR, Frederick, MD). The transduced cells were enriched in medium containing 200 μg/mL Geneticin (Invitrogen, Grand Island, NY) for 10 days and sorted by FACs to select for a pure population using the BD FACSVantage™ (BD Bioscience, San Jose, CA).
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8

Sorting of Dct-GFP Melanoblasts/Melanocytes

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iDct-GFP-positive melanoblasts/melanocytes were sorted using the BD FACSAria IIu or BD FACS Vantage (BD Biosciences) systems. FACS DIVA software was used during cell sorting and the FlowJo software for analysis. Cells were initially identified on forward scatter (FSC) vs. side scatter (SSC). Single cells were identified using FSC and SSC pause width. Cell doublets were excluded from the analysis. Embryos of the same developmental age that were heterozygous for the TRE-H2B-GFP gene but lacked the Dct-rtTA gene were used as negative controls. Cells were sorted based on GFP expression and SSC-A. GFP-positive cells were identified using appropriate gates based on negative controls. Due to low sample cell number, reanalysis of sorted cells was not usually done, but representative post-sort analyses confirmed that presort purities of 0.74–0.75% were enriched to 98–99.5%.
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9

Flow Cytometry Analysis of Murine and Zebrafish Cells

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For mice, the following antibodies were used: Alexa Fluor 647 anti-CD144 (eBioBV13), PE anti-CD45 (30-F11), PE-Cy7 anti-CD31 (390), APC- eFluor 780 anti-c-kit (2B8), PE-anti-ESAM (1G8/ESAM), APC anti-CD19 (1D3), PE-Cy7 anti-B220 (RA3-6B2), PE-Cy anti-Thy1.2 (53-2.1), APC-C7 anti-CD25 (PC61), PerCP-Cy5.5 anti-Gr-1 (RB6-8C5), PE anti-CD3ɛ (145-2C11), APC-Cy7 anti-Mac-1 (M1/70), FITC anti-CD45.2 (104), PE-Cy7 anti-CD45.1 (A20), PerCP-Cy5.5 anti-Sca1 (D7), eFluor 450 lineage-specific cocktail [(anti-TER119 (TER119), anti-Gr-1 (RB6-8C5), anti-B220 (RA3-6B2), anti- CD3 (17A2), and anti-Mac-1 (M1/70)], APC anti-CD34 (MEC14.7), PE anti-Flt3 (A2F10), PE anti-IFNgr1 (2E2, Abcam), APC anti-CD48 (HM48-1), and PE-Cy7 anti-CD150 (TC15-12F12.2). DAPI was used to exclude dead cells. Cells were sorted on a BD FACSvantage at low speed and low pressure (North et al. 2002 (link)) and analyzed on a BD LSR II flow cytometer; data were analyzed with FlowJo (Tree Star).
For zebrafish, transgenic embryos (five per sample with four or more replicates) were incubated in 0.5 mg/mL Liberase (Roche) solution with gentle agitation for 90 min at 37°C and then dissociated, filtered, and washed with PBS. Dead cells were excluded by 5 nM SYTOX red (Life Technologies) prior to analysis using a BD FACS Canto II or Beckman Coulter Gallios. Cell sorting was performed using a Beckman Coulter MoFlo XCP.
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10

Annexin-V/PI Apoptosis Assay in NRVMs

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The NRVMs were harvested after indicated treatments with trypsin (0.25%) and a single cell suspension prepared. Cells were then washed with PBS and pelleted by centrifugation at 1200 rpm for 5 minutes. Cells were resuspended in binding buffer and the cell density was adjusted to 5 × 105 cells ⁄ ml. A 95-µL aliquot of the cell suspension was added to 5 µL Annexin-V-FITC, and then cells were incubated for 10 minutes at room temperature in the dark. The suspension was then washed with PBS and resuspended in 190 µL binding buffer before adding 10 µL propidium iodide (PI) to obtain a final concentration of 1 µg ⁄mL PI. The samples were examined by flow cytometry (BD FACSVantage; BD Sciences, San Jose, CA, USA). The results were analyzed using cell quest software (BD Sciences) to determine the rate of apoptosis in the lower right quadrant.
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