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25 protocols using dynabeads cd3

1

Rat Prefrontal Cortex Dissection and T-Cell Isolation

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The rat PFC was dissected following isoflurane anesthesia and decapitation and was defined as Bregma +2.5 to +4.2, +2 mm on either side of the midline and a depth of 5 to 6 mm from the dorsal surface of the cortex. This region, corresponding to the rat mPFC, encompasses the prelimbic and infralimbic subregions and is the closest functional equivalent of the human dorsolateral prefrontal cortex63 (link). Brain imaging studies have demonstrated that chronic pain is associated with altered structure, function and connectivity of the human DLPFC4 (link)65 (link). T cells were isolated from the PBMCs by immunomagnetic isolation using CD3+ Dynabeads (Life Technologies, Burlington, ON, Canada) as previously described11 (link). CD3 polypeptides play pivotal role in intracellular assembly, surface expression, and signal transduction via the pre-T-cell receptor (pre-TCR) and TCR complexes. CD3 chains are required for thymocyte differentiation and are expressed in virtually all-mature T cells66 (link). T-cell and brain DNA and RNA were extracted using the AllPrep DNA/RNA Qiagen kit (Hilden, Germany) and were quantified using the Qubit system (Life Technologies, Burlington, ON, Canada).
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2

Epigenetic Profiling of T Cells in Breast Cancer

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CD3+ T cells were isolated from 8 ml blood drawn from age matched control women and women at different stages of breast cancer using CD3 dynabeads (Life Technologies, Toronto, Ontario, Canada). Following the extraction of T cells, DNA was extracted using AllPrep DNA/RNA mini kit (Qiagen, Canada) and whole genome DNA methylation profiles were generated using Illumina 450 K bead arrays.
All the peripheral whole blood samples were stored in EDTA tubes at 4 °C until Leukocyte isolation. Leukocytes were freshly isolated from whole blood by using ficoll gradient separation. The leukocyte cell pellets were immediately frozen at − 80 °C until further use. First, B cells were positively isolated using a Dynabeads CD19 positive isolation kit (Invitrogen). Subsequently, these B cell-depleted leukocytes were used for T-cell purification with a Dynabeads CD3 positive isolation kit (Invitrogen). The T-cell pellets were immediately frozen at − 80 °C for further DNA isolation. DNA was isolated from different blood cell types using AllPrep DNA/RNA mini kit from Qiagen.
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3

PBMC Isolation and T Cell Purification

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This was performed as previously described.35 (link) In brief, peripheral blood was drawn into EDTA-coated tubes. PBMCs were isolated through centrifugation with Ficoll-Paque (GE Healthcare, Burnaby, BC, Canada), and T cells were isolated from the PBMCs using CD3+ Dynabeads (Life Technologies, Burlington, ON, Canada).
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4

CD3+ T Cell Isolation from Monkey Blood

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Separation of CD3+ T cells from monkey peripheral blood was performed as described previously (Provencal et al., 2012 (link)). In brief, peripheral blood was drawn into EDTA-coated tubes. Peripheral blood mononuclear cells (PBMCs) were isolated through centrifugation with Ficoll-Paque (GE Healthcare, Burnaby, BC, Canada), and T cells were isolated from the PBMCs using CD3+ Dynabeads (Life Technologies, Burlington, ON, Canada).
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5

NK Cell Cytotoxicity Assay Protocol

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NK cells were isolated from healthy donors using column-based magnetic cell sorting by CD56+ microbeads (Miltenyi Biotech, Bergisch Gladbach, Germany) after previous CD3+ TCD of PBMCs by CD3+ dynabeads (Life Technologies, CA) according to the manufacturers’ protocols. NK cells were seeded in 96-well round-bottomed microplates at different effector to target ratios (E:T ratio) and incubated for 22 hours with 0, 2, or 1000 μg/mL ATLG. K562 target cells were labeled with BATDA (PerkinElmer, MA) and, after 3 washing steps, cocultured with ATLG-preincubated NK cells for 2 hours. Fluorescence of Europium-TDA chelates of supernatants was quantified using a VICTOR multilabel reader (Wallac, Finland).
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6

Isolation of Tonsillar B Cell Subsets

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Tonsillar B cells were isolated using negative isolation with CD3 Dynabeads (Thermo Fisher, MA, USA). CD3-depleted cells were split in two populations and incubated with antibodies for 10 min. CD44- GC B cells were obtained through negative selection by combining Biotin Binder Dynabeads (Thermo Fisher, 50 μl beads per 10x106 cells) with biotinylated anti-CD44 (BD Pharmingen) (1:50). A naïve/memory joint population was isolated using Biotin Binder Dynabeads (Thermo Fisher) with biotinylated anti-CD38 (eBioscience) (2.35 μg/mL). Cells and Dynabeads were incubated in the dark at 4°C with rotation. IgD-depleted memory B cells were obtained by negative selection by incubating CD19+ B cells with Pan Mouse IgG Dynabeads (Thermo Fisher) coated with mouse anti-human IgD Abs (BD) for 30 min at 4°C, followed by removal of beads.
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7

Tumor-infiltrating T cell enrichment

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Tumors were injected with PBS, VNP20009 and two flagellum-deficient strains, and were resected after 6 days. The tumor mass was dissected and incubated in PBS containing collagenase I (Gibco), collagenase IV (Sigma–Aldrich), DNase I (Sigma–Aldrich) and hyaluronidase (Worthington) for 1 h at 37 °C. Then the cell suspension was filtered through a 70 μm cell strainer (Corning). Tumor-infiltrating T cells were enriched using CD3 Dynabeads (Thermo Fisher Scientific) according to manufacturer's instructions. In brief, 1 × 107 total tumor cells were suspended in 1 mL isolation buffer, and incubated with 25 μL CD3 Dynabeads for 20 min at 4 °C. The tube was placed in a magnet for 2 min. Then the supernatant containing unwanted tumor cells were discarded. The magnetic beads were washed 3 times with cold PBS. The enriched CD3+ T cells were lysed for RNA extraction by adding cell extraction buffer of Trizol Plus kit (Invitrogen) to the magnetic beads.
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8

Isolation and Depletion of CD3+ T Cells from PBMCs

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PBMCs were isolated from healthy donors by density gradient centrifugation using Biocoll separating solution (Biochrom GmbH, Berlin, Germany) after informed consent. CD3+ cells were subsequently depleted by CD3 Dynabeads (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. CD3-depleted PBMCs were seeded at a cell density of 1.0 × 106 in 25 ml culture flasks in RPMI 1640 medium (Biochrom) supplemented with 10% fetal bovine serum (Biochrom), 2 mM L-glutamine (Biochrom), 100 U/ml penicillin (Biochrom), and 100 μg/ml streptomycin (Biochrom) in the presence of 5% CO2 in a humidified atmosphere at 37 °C. All experiments involving human tissues were approved by the ethics committee at the Medical Faculty of the Eberhard Karls University and the University Hospital Tuebingen (349/2013BO) and informed consent was obtained from healthy donors in accordance with the Helsinki Declaration of 1975 (revised in 2008).
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9

Isolation and Proliferation Analysis of T Cell Subsets

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Buffy coats were obtained from healthy volunteers, with approval by the local ethical committee (Landesaerztekammer Rheinland-Pfalz). CD8+ T cells, CD4+CD25 and CD4+CD25+ T cells were isolated as previously described.[14 (link), 44 (link), 45 (link)] For some experiments, peripheral blood mononuclear cells (PBMC) were depleted of T cells using CD3-Dynabeads (0.5 beads/cell, Invitrogen).
For proliferation assays, cells were labeled with carboxyfluorescein succinimidyl ester (CFSE) and cultured in 48 well plates at 106 cells/ml, stimulated with 0.5 μg/ml anti-CD3 mAb (clone OKT3) plus 1 μg/ml anti-CD28 mAb (clone 28.2, eBioscience) in presence or absence of different ratios of melanoma cells.
To analyze the effect of sGARP on proliferation and granzyme B expression of CD8+ T cells, T cells were stimulated with anti-CD3 mAb (0.5 μg/ml) and anti-CD28 mAb (1 μg/ml) or with melanoma cell line D05-MEL#6 (5 × 104/ml) in presence or absence of sGARP (10 μg/ml) from R&D Systems (#6055-LR, <0.01 endotoxin units per 1 μg) as shown before.[9 (link)] At day 7, T cells were harvested and re-stimulated with melanoma cells or anti-CD3 mAb (0.5 μg/ml) plus irradiated (90 Gy) T cell-depleted PBMC. For some experiments, T cell proliferation was measured by additional 16h-pulse with 3H TdR (37 kBq/well) using a liquid beta-scintillation counter.
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10

T Cell Proliferation Assay with Monocytes

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CFSE labeled CD4 T cells (1×105) were incubated with monocytes (2×104) in 96-well plates in complete RPMI medium. Cells were harvested at six hours, 2 days, and 5 days. After 6 hours of culture, harvested cells were enriched by depleting T cells with CD3 Dynabeads® (Invitrogen, Carlsbad, CA), and RNA was extracted for use in microarray testing. After two days of culture, cells were harvested, and monocytes were stained for different cell surface markers. After five days of culture, cells were harvested, and the CFSE dilution was measured to assess the level of T cell proliferation.
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