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19 protocols using cd44 apc cy7

1

Multi-Parametric Flow Cytometry and Molecular Analyses

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For multi-parametric flow cytometry, immunofluorescence/immunohistochemistry and DEPArray analyses, primary antibodies were obtained from the following sources: FITC-CD45 (#304054; 1:200), FITC-CD34 (#343504; 1:200), FITC-CD105 (#323204; 1:200), FITC-CD90 (#328108; 1:200), FITC-CD73 (#344016; 1:200), FITC HLA-A/B/C antibody (#311404; 1:200), PerCP/Cy5.5-CD146 (#342014; 1:100), PE-Human NG2/MCSP (#FAB2585P, 1:100), BV421-Ki67 (#350506; 1:100), were obtained from Biolegend, Inc. APC-Cy7-CD44 (#103028, 1:100) BV510-CD24 (#311126, 1:100), PE-Pan-Cytokeratin (#5075, 1:100) were purchased from Cell Signaling Technology, Inc. Anti-Mel-A antibody (# AC12-0297-03; 1:200) was obtained from Abcore, and FITC-Anti-S100 (#ab76749; 1:50) was purchased from Abcam. For immunohistochemistry, anti-human, anti-Mel-A antibody (# ab51061; 1:100), HLA-ABC (#565292; 1:100) were obtained from BD Biosciences, Inc. (San Jose, CA, USA). Anti-mouse secondary IgG anti-human antibodies used for IHC staining were received from Santa Cruz Biotechnology, Inc. Antibodies for immunofluorescence staining were obtained from Cell Signaling Technology, Inc. (1:500 dilution of stock solution), as previously described [3 (link),22 (link)]. NRF2 inhibitor ML385 (#2114) was obtained from Cayman, Inc. while Nodal inhibitor Lefty (746-LF/CF) was purchased from R&D Systems, Inc. (Waltham, MA, USA).
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2

Multiparametric Flow Cytometry and Immunohistochemistry

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For multiparametric flow cytometry, conjugated antibodies FITC‐CD45 (#304054; 1 : 200), FITC‐CD34 (#343504; 1 : 200), FITC‐CD105 (#323204; 1 : 200), FITC‐CD90 (#328108; 1 : 200), FITC‐CD73 (#344016; 1 : 200), FITC HLA‐A/B/C (#311404; 1 : 100), APC‐Cy7‐CD44 (#103028; 1 : 100), BV650‐CD44 (#103049; 1 : 100), and AF647‐Pan‐CK (#628604; 1 : 100) were obtained from BioLegend (San Diego, CA, USA); PE‐Pan‐CK (#5075; 1 : 100) antibody was received from Cell Signaling Technology (Danvers, MA, USA).
For immunohistochemistry, primary antibodies were obtained from the following sources: Anti‐human cocktail of gross cystic disease fluid protein‐15 (GCDFP‐15) + mammaglobin (#906H‐08; 1 : 200) was obtained from Sigma‐Aldrich (St. Louis, MO, USA); CD44 (#960‐MSM2‐P0; 1 : 200) and Pan‐CK (#MSM2‐371‐P0; 1 : 200) antibodies from NeoBiotechnologies (Union City, CA, USA); and Alexa Fluor‐conjugated anti‐mouse, anti‐rabbit secondary IgG antibodies (1 : 500) from Cell Signaling Technology.
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3

Peptide Library Synthesis and Liposome Formulation

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Trp2, AH1 and WT1 peptide libraries and peptides were synthesized by GenScript. CoPoP was synthesized as previously reported (32 (link)). The following lipids were used to produce liposomes: dioleoylphosphatidylcholine (DOPC; Corden #LP-R4–070), cholesterol (PhytoChol; Wilshire), and synthetic PHAD-3D6A (Avanti; #699855). QS-21 was purchased from Desert King (part number NC0949192). The APC-CD8a (Clone: CT-CD8a) antibody was obtained from Accurate Chemical and Scientific Corporation (#ACL168APC). The following antibodies were obtained from BioLegend: APC-CD8a (Clone: CT-CD8a; #100712), FITC-CD4 (Clone: GK1.5; #100405), AF700-CD45 (Clone: 30-F11; #103127), APC-Cy7-CD44 (Clone: IM7; #103027), PE/Cy7-CD62L (Clone: MEL-14; #104417), PerCP-Cy5.5-PD-1 (Clone: RMP1–30; #109119), pacific blue-IFN-γ (Clone: XMG1.2; #505818), BV605-TNF-α (Clone: MP6-XT22; #506329), PE/Cy7-Granzyme B (Clone: QA16A02; #372213). Anti-mouse PD-1 (#BP0146) and anti-mouse CTLA-4 (#BP0131) were acquired from Bio X Cell. Other reagents used were Golgiplug/Brefeldin A (BD; #555029), Live/Dead dye (Invitrogen; #L34857), Fc-block (Clone: 2.4G2; BD #553142), fixation/permeabilization kit (BD #554714), red blood cell (RBC) lysis buffer (BioVision #5830), Collagenase Type I (Gibco #17018–029), and DNase I (Roche #04536282001).
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4

Immune Phenotyping of Extracellular Vesicles

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The immune phenotype of EVs was analyzed using flow cytometry (BD FACS Aria III, BD Bioscience, East Rutherford, NJ, USA) by immunostaining with the CD49e-PE (Sony, Tokyo, Japan), CD63-FITC (Biolegend, San Diego, CA, USA), Sca1-APC/Cy7 (BioLegend), CD45-PE/Cy7 (BioLegend), CD9-APC (Biolegend) and CD44-APC/Cy7 (BioLegend) antibodies.
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5

Multicolor Flow Cytometry Analysis

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Direct immunofluorescence cell staining was performed using the following cell surface marker antibodies: CD4-FITC, CD8-APC, CD44-APC/Cy7, and CD62L-PacificBlue (all BioLegend, San Diego, CA). Stained cells were analyzed using a FACSAria (Beckton-Dickinson, Mountain view, CA). FACS data were analyzed using FCS Express V3 (De Novo Software, Los Angeles, CA) software.
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6

Dissecting Murine Lymphoid Cell Subsets

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Lymphoid cells from bone marrow, thymus and spleen were isolated from 8-week old mice. To reveal T cell progenitor subsets in the thymus, single cell suspensions were stained with conjugated antibodies, specific for CD3-FITC (Biolegend), CD4-APC, CD8a-PerCp-Cy5.5, CD25-PE, CD44-APCCy7 (Biolegend), TCRβ-Pacific Blue (Biolegend). To analyse lymphoid subsets in the spleen, single cell suspensions were stained with CD3-FITC, CD4-APC, CD8a-PerCp-Cy5.5, CD19-APCH7, CD45R(B220)-PacificBlue, IgD-PE (eBioscience), IgM-PECy7 (eBioscience). To define the B cell progenitor subsets, suspensions from the bone marrow were stained with IgD-FITC, CD25-PE, IgM-PECy7 (eBioscience), CD45R (B220)-PacificBlue, CD117 (cKit)-APC (eBioscience), CD19-APCH7. Dead cells were excluded from the analysis by propidium iodide staining. Antibodies were purchased from BD Pharmingen unless mentioned otherwise. Samples were measured on a FACS Fortessa® and analysed using FlowJo® software (Version: 10.0.8r1).
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7

Characterization of Tumor Cell Populations

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Tumors were dissected from the lungs of TKO Hes1GFP/+ mice approximately 5–7 months after tumor induction and digested as previously described40 (link). The antibodies used were: CD45-PE-Cy7 (eBioscience, clone 30-F11, 1:100), CD31-PE-Cy7 (eBioscience, clone 390, 1:100), TER-119-PE-Cy7 (eBioscience, clone TER-119, 1:100), CD24-APC (eBioscience, clone M1/69, 1:200), Ncam1 (Cedarlane, clone H28-123-16, 1:100), anti-rat-IgG2a-PE (eBioscience, clone r2a-21B2, 1:200), EpCam (eBioscience, clone G8.8, 1:100), CD44-APC-Cy7 (BioLegend, clone IM7, 1:100). 1 μg/mL 7-aminoactinomycin D (Invitrogen) or DAPI was used to label dead cells.
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8

T-cell Marker Analysis in Lck-Dlx5 Mice

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Flow cytometry was performed with a LSRII machine (Becton Dickinson) to analyze T-cell developmental and cell death markers from healthy Lck-Dlx5 mice. CD4-APC/Cy7, CD8-PE, CD44-APC/Cy7, CD25-PE, Notch1-Alexa647 and Notch3-APC antibodies were obtained from BioLegend. Annexin V-FITC and ethidium homodimer III were from Biotium. Data were analyzed with FlowJo software.
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9

Optimizing Mesenchymal Stem Cell Isolation

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Collagenase type I, penicillin/streptomycin (Pen/Strep) broad-spectrum antibiotic cocktail, trypsin-EDTA (0.25%), fetal bovine serum (FBS), human insulin and Dulbecco’s Modified Eagle’s Medium (DMEM) were purchased from Gibco/Invitrogen (Carlsbad, CA, USA). VersaLyseTM was purchased from Beckman Coulter (Miami, FL, USA). Dexamethasone, 3-isobutyl-methylxanthine, Nile Red (NR) and indomethacin were purchased from Sigma-Aldrich (St. Louis, MO, USA). Vybrant® DyeCycleTM Violet was purchased from Thermo Fisher Scientific/Life Technologies (Eugene, OR, USA). The following mouse anti-human monoclonal antibodies were purchased from Biolegend (San Diego, CA, USA): CD14-APC Cy7 (Clone M5E2), CD31-PE Cy7 (Clone WM-59), CD36-APC (Clone 5-271), CD73-FITC (Clone AD2), CD44-APC Cy7 (Clone IM7) and CD105-PE (Clone 42A3). Mouse anti-human CD45-Krome Orange (Clone J.33), CD90-PE-Cy5 (Clone Thy-1), CD34-PE Cy7 (Clone 581), and the viability dye, 7-aminoactinomycin D (7-AAD) were purchased from Immunotech/Beckman Coulter (Marseille, France).
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10

Isolation and Characterization of Murine MSCs

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MSCs were isolated from subcutaneous adipose tissue of the adult mice (8–9 weeks old). Adipose tissue were dissected into small pieces and digested with 0.2% collagenase II (Dia-M, Russia) in a shaker-incubator at 37 °C, 120 rpm for one hour. Suspended cells were pelleted (500 g for 5 min), washed once in PBS (PanEco, Russia) and re-suspended in DMEM (PanEco, Russia) supplemented with 10% fetal bovine serum (Gibco, UK) and 2 mM l-glutamine (PanEco, Russia). MSCs were maintained at 37 °C, 5% CO2 with culture medium being replaced every 3 days. MSCs from passages 3 and 4 were used for the experiments.
MSCs were differentiated into three lineages: adipogenic, chondrogenic and osteogenic and it was confirmed by detection of lipid droplets (Oil Red dye staining), glycosaminoglycans and mucins (1% alcian blue staining) and calcium deposits (5% AgNO3 staining), respectively. Immune phenotype was determined using monoclonal antibodies to CD90.2-PerCP (1301575; Sony, USA), CD44-APC/Cy7 (103028; BioLegend, USA), CD73-Alexa Fluor647 (127208; BioLegend, USA), CD49e-PE (1119525; Sony, USA), Sca1-APC/Cy7(108126; BioLegend, USA), CD29-PE (102208; BioLegend, USA), CD11b-PE/Cy7 (101216; BioLegend, USA), CD10-PE (312203; BioLegend, USA), CD45-PE/Cy7 (103114; BioLegend, USA). Expression of CD markers was analyzed by flow cytometry (BD FACS Aria III (BD Bioscience, USA)).
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