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9 protocols using facs aria 1 sorter

1

Isolation and Characterization of Human Tregs

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Peripheral blood mononuclear cells (PBMCs) were isolated from blood of patients or from the buffy coat preparations of healthy donors by standard Ficoll-Paque™ Plus density-gradient centrifugation (GE Healthcare). PBMCs were labeled with anti-CD4, anti-CD127, anti-CD25, and anti-CD45RA monoclonal antibodies, incubated at 4°C in the dark for 20 min. For intracellular staining, cells were permeabilized with 150 μL of fixation/permeabilization solution at 4°C for 12 h. After two washes with permeabilization buffer 1×, PBMCs were incubated with anti-FOXP3 and anti-Helios for 30 min at 4°C in the dark. Samples were acquired with an Attune® Acoustic Focusing Cytometer (Life Technologies) and FlowJo 7.6.2 software (Tree Star, Ashland, OR, USA) was used for data analysis. A total of 100,000 events were acquired for analysis, after gating of lymphocytes based on the FSC/SSC dot plot.
For sorting, 50 × 106 PBMCs were washed once and resuspended in media (RPMI/10% FBS) at 100 × 106 per ml. Cells were incubated with anti-CD4 and anti-CD25 at 4°C for 30 min, washed twice and resuspended in PBS 1×. Labeled cells were sorted using a FACs Aria I sorter (BD Biosciences). For Treg isolation, a CD4+CD25veryhi gate was used and sorted cells were collected in media (RPMI/20% FBS), washed once and resuspended in culture media until ready to be plated in the suppression assay.
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2

Isolation and Analysis of Human Regulatory T Cells

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Tregs were identified as CD4+/CD25+/FoxP3 positive cells by flow cytometry analysis. The staining was performed using Treg detection human kit (Miltenyi Biotech, Bergisch Gladbach, Germany) and the results analyzed by BD CANTO II flow cytometer and DIVA software (Becton-Dickinson, Franklin Lakes, New Jersey, USA). A total of 100,000 events were acquired for analysis after gating of lymphocytes based on the FSC/SSC dot plot. For sorting, labeled cells were sorted using a FACs Aria I sorter (BD Biosciences). For Treg isolation, a CD4+CD25veryhi gate was used, and sorted cells were collected in media (RPMI/20% FBS), washed once, and suspended in culture media.
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3

Isolation and Sorting of Human NK Cells

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Peripheral venous blood samples were collected in heparin-containing tubes, and PBMCs were isolated by density-gradient centrifugation using Ficoll-Paque Plus solution (Amersham Biosciences, Uppsala, Sweden). NK cells were phenotypically identified as CD3-CD56+ cells by flow cytometry, as previously described [21 (link),22 (link)]. NK cells were isolated using CD56 MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of CD3-CD56+ cells was greater than 95% as analyzed by flow cytometry. For sorting of CD69+ and CD69- NK cells, PBMCs were stained with APC-conjugated anti-CD3, FITC-conjugated anti-CD56, PerCP-conjugated anti-CD45, and PE-conjugated anti-CD69 mAb, and were sorted to obtain CD45+CD3-CD56+CD69+ and CD45+CD3-CD56+CD69- NK cells using a FACS Aria I sorter (BD Biosciences, Mountain View, CA) at purities of > 98%.
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4

Alpharetroviral vector construction for XCGD-iPSCs

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A. Schambach (Medizinische Hochschule Hannover, Hannover, Germany) kindly provided the alpharetroviral backbone vector containing CO CYBB cDNA.11 (link) Construction of a series of alpharetroviral vectors (Supplementary Fig. S1; supplementary data are available online at http://online.liebertpub.com/hgtb) is described. The production of viral supernatant is described.12 (link) In the case of XCGD-iPSCs, cells were first maintained under feeder-free conditions before virus transduction at the desired multiplicity of infection. To obtain clonal populations of transduced XCGD-iPSCs, dissociated cells were singly sorted by flow cytometry (FACSAria I sorter; BD Biosciences, San Jose, CA) into 96-well plates. Sorted cells were then expanded and maintained. All transduced XCGD-iPSCs and PLB cells were maintained under constant puromycin (Thermo Fisher Scientific) selection pressure to ensure retention of transgene-positive cells.
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5

Phenotyping Antigen-Specific T Cells

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Cryopreserved PBMC were thawed into medium containing DNAse (50 IU/mL, Sigma-Aldrich), washed and stained with Violet or Aqua LIVE/DEAD Fixable Dead Cell Stain (Thermo-Fisher Scientific). Cells were then stained with anti-CCR7 anti-body at 37°C for 20 min, washed and then stained with 2 µg/mL MHC class II-CFP10 tetramers (DRB1*04:01-CFP-1071–85, DRB5*01:01-CFP-1051–65) at room temperature (RT) for 1 h. Cells were washed and stained with surface marker antibodies, according to Table S1 in Supplementary Material, for 40 min at RT in a total volume of 100 µL. Samples were acquired and sorted on a BD Bioscience FACS Aria I sorter using FACS DIVA software (Version 6).
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6

Isolation of Naïve CD8+ T Cells

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Naïve CD8+ T cells were sorted using a FACSAria I Sorter (BD Biosciences) by staining the isolated PBMCs with anti-CD8 FITC (BD Biosciences), anti-CD197 (CCR7) PE, anti-CD95 APC (both from BioLegend), anti-CD45RO PE-Cy7, anti-CD45RA BV421 and 7-Amino-Actinomycin D (7-AAD) (all from BD Biosciences). PBMCs were sorted into naïve T cells (TN, CD8+ CD197+ CD95- CD45RO- CD45RA+), collected into RPMI 1640 medium containing 1% FBS and counted manually before starting the differentiation experiments.
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7

Generating Allogeneic Tolerogenic DCs

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CD14+ monocytes were isolated from PBMCs by positive selection using magnetic MicroBeads (Miltenyi Biotec, Bergisch Gladbach, NRW) according to the manufacturer's protocol and washed twice with RPMI medium. The CD14+ cells (1–2 × 106) were cultured for 8 days in RPMI medium supplemented with 10% human AB serum, 50 ng/ml of GM-CSF, and 50 ng/ml of IL-4 into 48-well plates. Monocyte-derived dendritic cells (Mo-DCs) were irradiated with 3,000 rads prior to the functional assays.
For naïve T cell isolation, PBMCs from other healthy individual (allogeneic) were stained with anti-CD4, anti-CD25, and anti-CD45RA monoclonal for 20 min at 4°C in the dark, washed twice with phosphate-buffered saline (PBS) and resuspended in PBS. A CD4+CD25CD45RA+ gate was used for sorting naïve T cells using the FACS Aria I sorter (BD Biosciences). The sorted cells were collected in culture medium RPMI 20% FBS, washed twice with PBS 1×, stained with CTV, and resuspended in OpTmizer™ CTS™ T-Cell Expansion culture medium (Thermo Fisher Scientific). Subsequently, CTV-labeled naïve T cells were co-cultured for 7 days with irradiated allogeneic Mo-DCs (naïve T cells: Mo-DC ratio of 10:1) in culture medium supplemented with 5 ng/ml TGF-β1, 100 U/ml IL-2, and 10 nM ATRA (Sigma-Aldrich) into 96-well U bottom plates.
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8

Isolation and Identification of MAIT Cells from Human Blood

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Peripheral venous blood samples were collected in heparin-containing tubes, and PBMCs were isolated by density-gradient centrifugation using Ficoll-Paque Plus solution (Amersham Bioscience, Uppsala, Sweden). MAIT cells were identified phenotypically as CD3+TCRγδ-Vα7.2+CD161high by flow cytometry as previously described [10 (link), 24 (link), 45 (link)]. Total lymphocyte numbers were measured by Coulter LH750 automatic hematology analyzer (Beckman Coulter, Miami, FL). Absolute numbers of MAIT cells were calculated by multiplying the MAIT cell percentages by the CD3+γδ- T cell percentages and the total lymphocyte numbers (per microliter) in peripheral blood. For sorting of MAIT cells, PBMCs were stained with PE-conjugated anti-CD3, FITC-conjugated anti-TCR γδ, APC-conjugated anti-TCR Vα7.2 and PE-Cy5-conjugated anti-CD161 and sorted to obtain CD3+TCRγδ-Vα7.2+CD161high MAIT cells using a FACS Aria I sorter (BD Biosciences, Mountain View, CA). MAIT cells were isolated at purities of > 98%.
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9

Quantifying Colonic Th Cell miR-148a

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CD3+CD4+ Th cells from the colonic lamina propria were sorted using a FACSAria I sorter (BD Biosciences). Cells were lysed and total RNA was purified with the Quick-RNA MiniPrep kit (Zymo Research). Mature miR-148a and U6 small nuclear RNA (snRNA) were detected by quantitative PCR with the Taqman MicroRNA Reverse Transcription kit in combination with TaqMan MicroRNA Assays (Applied Biosystems) according to the manufacturer's recommendations. For normalization, the expression values were compared to values of snU6 RNA by the change-in-threshold method (2−ΔCT).
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