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9 protocols using neutrophil isolation kit

1

Isolation and Characterization of Low-Density and Normal-Density Neutrophils from Cord Blood

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We isolated mononuclear cells and granulocytes, as reported above, from three different CB samples. From the mononuclear cell fraction, we isolated LDNs by performing a double round of magnetic bead sorting using Neutrophil Isolation kit (Stemcell technologies). From the granulocyte cell fraction, we isolated NDNs by performing a single round of magnetic bead sorting using Neutrophil Isolation kit (Stemcell technologies). To ensure a sufficient representation of neutrophil precursors (less abundant cell population) and of NDNs (less efficiently detected by droplet-based scRNA-Seq due to loe RNA content), LDNs and NDNs from each CB sample were mixed in a ratio of 1:3. We plated LDN-NDN mix at 106 (link) cells/ml in RPMI 1640 + 10% FBS + 1% Gln + 1% Pen/strep alone or with G-CSF, IFN-β or IFN-g all used at 10ng/ml. After 4h, cells were harvested, washed, counted and for each condition we mixed cells from different CB in a ratio 1:1:1. The pooled samples were processed for scRNAseq as described below. A detailed reagent list is reported in Supplementary Table 44.
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2

Neutrophil Transwell Migration Assay

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Murine neutrophils were isolated from mouse bone marrow using a neutrophil isolation kit (Stemcell Technologies) per manufacturer’s protocol. After cell viability was checked by trypan blue, neutrophils were suspended in DMEM-1% endotoxin-free BSA-10 mM HEPES and 200,000 cells were placed in the upper insert of a 12-well Transwell chamber (5-μm pore size, 6.5-mm diameter; Costar Corning). The supernatant from bone marrow-derived WT macrophages stimulated with sonicated S. Typhimurium or Macrophage Inflammatory Protein-2 (MIP-2) at 5 ng/ml were applied to the bottom well. After 60-min incubation at 37°C in 5% CO2, the cells in the bottom well were harvested by adding 50 μl of 70 mM EDTA and counted with a hemocytometer.
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3

Isolation and Culture of Murine and Human Immune Cells

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Isolation and culture of murine lamina propria mononuclear cells (LPMC) and mesenteric lymph node (MLN) cells were carried out as previously reported(18 (link)). MLN and LPMC were cultured in 96-well round-bottom plates at 1.5 × 106 cells/mL of RPMI 1640 containing 2mmol/L glutamine and 25 mmol/L HEPES (Corning), 10% fetal bovine serum (Omega Scientific, Inc.), 100 μM NEAA (Gibco), 1 mM sodium pyruvate (Fisher), 10 ng/ml LPS (InvivoGen), 50 μM β-mercaptoethanol (Sigma), 50 μg/mL gentamicin (Gemini). Media were harvested 48 hours after culture and assessed for Il1β and Tnfα production via ELISA kit (eBioscience) per manufacturer’s protocol. Mouse bone marrow derived macrophages (BMM) and subsequent differentiation to M1 and M2 macrophages were performed as described (20 (link)). Murine neutrophils were isolated from mouse bone marrow using a neutrophil isolation kit (Stemcell Technologies) per manufacturer’s protocol. Human peripheral blood monocyte derived macrophages (PBM) were obtained by first isolating monocytes as previously described (21 (link)). Isolated monocytes then underwent M1 and M2 differentiation condition as previously described (20 (link)). For human studies, paired samples (WT and ATG16L1 T300A) were obtained for each PBM isolation and differentiation at same day.
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4

Neutrophil Isolation and Functional Analysis

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To confirm the presence of neutrophils in the human entheseal tissue, cells released following enthesis digestion (n=3), described above, were incubated with 10% mouse serum and 1% IgG in FACS buffer prior to incubation with antibodies. Cells were then stained with DAPI (live/dead), CD45+ (leukocytes), CD66b+ (granulocytes) and CD16+ (neutrophils). Cells were analyzed using the FACSMELODY (BD Biosciences) and FlowJo software (Tree Star Software, San Carlos, California, USA). All lists of antibodies, clones and manufacturers can be found in the supplementary material (Supplementary Table 1). For functional studies, neutrophils were isolated from digested entheseal tissue using a neutrophil isolation kit (STEMCELL Technologies, Cambridge, MA). This kit was validated for neutrophil purity prior to proceeding with fungal adjuvant stimulation. After 48 h of culture, isolated neutrophils evaluated through flow cytometry show 94% purity for CD66b. Isolated entheseal neutrophils were subsequently cultured in RPMI (Sigma-Aldrich) supplemented with 10% FCS and 1% penicillin/streptomycin (Invitrogen). 5x105 neutrophils were plated in 96-well plates and stimulated with Zymosan (0.5mg/ml) (Sigma-Aldrich), IFNγ (20 ng/ml) (Peprotech) or Zymosan plus IFNγ for 48 h (n=4). The supernatant was then probed for IL-23 secretion by ELISA (ThermoFisher) according to the manufacturer’s instructions.
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5

Neutrophil Response to Fracture Supernatant

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Neutrophils are enriched to 82.7% purity (Supplementary Fig S1E) using a neutrophil isolation kit according to manufacturer's instructions (Stem Cell Technology) and incubated in 180 μl murine fracture supernatant + 10% FCS + 1% penicillin/streptomycin at 37°C, 4% CO2, and a density of 275,000 cells per well in a 96-well plate. rhTNF or PBS (in 20 μl) is added at 30 min. Cells and supernatants are harvested at 1 h. Protein levels of mCCL2 cytokine in the supernatants were analyzed as described above. Experiments were performed in triplicates.
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6

Intracellular Killing of Bacterial Pathogens

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To measure intracellular killing of MRSA, bone marrow neutrophils (mice) or blood neutrophils (humans) were purified with a neutrophil isolation kit (STEMCELL) and infected with either MRSA, K. pneumoniae, or P. aeruginosa at an MOI of 15 for 30 min. Gentamycin was then added to kill extracellular bacteria (0 time) (6 (link)). Survival of phagocytosed bacteria was determined by counting CFUs after incubation for the indicated times.
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7

Isolation and Co-culture of Immune Cells

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Monocytes and NK-cells were isolated from PBMCs using the Monocyte isolation kit and NK-cell isolation kit, respectively (Miltenyi Biotec, Germany). Neutrophils were isolated from HetaSep treated PBMC using Neutrophil isolation kit (both from Stem Cell Technology (BC, Canada). PKH26 (Sigma Aldrich) was used according to the protocol to label cell membranes when assessing membrane transfer between cells. NK-cells were mixed at a 1:1 ratio with either monocytes or neutrophils and IPH2101 was added at 1 μg/ml. Where indicated, IvIg or anti-FcyRI antibodies were added at a final concentration of 10 μg/106 cells prior to the assay to block FcyRs. At the end of assay, cells where stained with appropriate antibodies and acquired on a BD LSR II Fortessa.
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8

Isolation of Mouse Neutrophils

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Mouse bone marrows were isolated from donor mice and flushed to isolate bone marrow cells. Purified neutrophils were isolated using a neutrophil isolation kit from Stem cell technologies according to the manufacture’s protocol. This kit utilizes a negative selection method using magnetic beads.
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9

Neutrophil Isolation and FITC-Dextran Assay

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Neutrophil isolation kit (17957, STEMCELL, Vancouver, Canada); Bovine serum albumin (A1933-25G, Sigma-Aldrich, St. Louis, MO, USA), FBS (iCell-0500, iCell Bioscience Inc, Shanghai, China); RPMI 1640 (SH30809.01, Hyclone, Logan, UT, USA); Fluorescein (FITC-dextran, 10 kDa; final concentration 5 μM, Sigma-Aldrich, St. Louis, MO, USA); fMLP (F3506, 1 mM, Sigma-Aldrich, St. Louis, MO, USA); Triton X-100 (9036-19-5, Sigma, St. Louis, MO, MO, USA); Giemsa (G5637, Sigma, St. Louis, MO, USA); D-glucose (G7021, Sigma-Aldrich, St. Louis, MO, USA); mannitol (10 mM, an osmotic control reagent, M1902, Sigma-Aldrich, St. Louis, MO, USA); Fibronectin (F2006, 2 μg mL−1, Sigma-Aldrich, St. Louis, MO, USA); Commercial magnetic Neutrophil isolation kit (17957, STEMCELL Technologies, Inc., Toronto, Canada); Precursors and initiators of Polydimethylsiloxane (PDMS) (Dow Corning, Midland, MI, USA); Glass slide (80350-0001, Jiangsu Shitai Xinchuang Scientific Instrument Co., Ltd., Nanjing, China); Microscope (DMi8, Leica, Wezler, Hesse, Germany); Plasma cleaner (PDC-002, Harrick Scientific Products, Inc., New York, NY, USA).
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