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8 protocols using ki67 16a8

1

Comprehensive Immune Cell Profiling

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Cell surface and intracellular stainings were performed using antibodies as follows: CD4 (RM 4–5; BioLegend), CD8 (53–6.7; eBioscience), CD43 (1B11; BioLegend), CD62L (MEL-14; BioLegend), CD11b (M1/70; BioLegend), KLRG1 (2F1/KLRG1; BioLegend), Ki67 (16A8; BioLegend), FasL (MFL3; BD Biosciences), TRAIL (N2B2; eBioscience), Foxp3 (FJK-16s; eBioscience), GzmB (GB12; ThermoFisher Scientific), GzmA (GzA-368.5; eBioscience) and Gzm K (Orb102688; Biorbyt). Dead cells were excluded by fixable viability dye (eBioscience) staining. For FasL staining, lymphocytes were isolated and restimulated with anti-CD3 (145-2C11, eBioscience) and anti-CD28 (37.51, eBioscience) antibodies for 5 hours at 37 °C. BD Cytofix/Cytoperm Fixation/Permeabilization kit was used for intracellular staining following the manufacturer’s instructions. Data were acquired on an LSR II flow cytometer (BD Biosciences). Analyses were done using FlowJo 5.0 software (Tree Star Inc., Ashland, OR).
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2

Comprehensive Immunophenotyping Protocol

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The following clones of antibody were purchased from Biolegend (San Diego, CA, USA) and used for cell surface staining: CD4 (RM4-5), TCRβ (H57-597), NK1.1 (PK136), CD44 (IM7), CD24 (M1/69), CD127 (A7R34), CD69 (H1.2F3), CD25 (PC61), CD5 (53-7.3). For nuclear protein staining, cells were fixated and permeabilized using the FOXP3 transcription factor staining kit (Thermo Fisher Scientific, Waltham, MA, USA), according to the manufacturer’s instructions. The following antibodies were used: Ki67 (16A8) and PLZF (Mags.21F7) were purchased from Biolegend. Flow cytometry was performed on a FACSCanto II or FACSLSRII (BD Bioscience, San Jose, CA, USA) and analyzed with FlowJo software (version 10.8.1, BD Bioscience, San Jose, CA, USA). CD1d tetramer, either loaded or unloaded with αGC, was obtained from NIH Tetramer Core Facility (Atlanta, GA, USA).
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3

Comprehensive Treg Immunophenotyping Protocol

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Dead cells were stained using the fixable viability dye ZombieRed according to manufacturer’s instructions. Chemokine receptors CCR4 (clone 2G12), CXCR3 (CXCR3–173) and CCR5 (HM-CCR5) were stained for 1 hour at 37°C in cell culture medium. Staining for CD4 (GK1.5d), CD25 (PC61), CD44 (IM7), CD45 (30F11), CD62L (MEL14), ICOS (C398.4A), was performed at 4°C for 20 min. All these antibodies were from Biolegend. To detect intracytoplasmic and intranuclear antigens, cells were fixed and permeabilized using the Mouse Regulatory T cell Staining Kit from eBioscience, and stained for Ki67 (16A8, Biolegend), CTLA-4 (UC10-4B9, Biolegend), GFP/YFP (Alexa Fluor 488-conjugated polyclonal Rabbit IgG, Life Technologies), and Foxp3 (FJK-16s, eBioscience).
For some experiments, as indicated, blood-borne were distinguished from tissue-resident Treg by an i.v. injection of 3µg CD45.2-PE mAb (clone 104) 3 minutes before euthanasia.
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4

Multiparametric Flow Cytometry for Immune Cell Profiling

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Samples were analyzed using Aurora (Cytek) and LSR Fortessa (Becton Dickinson) flow cytometers and the resulting data were analyzed using FlowJo software (Tree Star, Inc). The following monoclonal antibodies were used from eBioscience, CD3ε (145-2C11); CD4 (GK1.5); CD8a (53-6.7); CD45 (30-F11); Foxp3 (FJK-16s). Helios (22F6) and Ki67 (16A8) were from Biolegend. GITR was from BD. Nrp1 was purchased from R&D Systems.
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5

Comprehensive Immune Cell Phenotyping

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Tissues were processed, single cell suspensions obtained, and cells were stained as described (Wherry et al., 2003). Cells were stained with LIVE/DEAD cell stain (Invitrogen) and with antibodies targeting KLRG1 (2F1/KLRG1, Biolegend), CD127 (A7R34, Biolegend), CD8 (53-6.7, Biolegend), CD44 (IM7, Biolegend), CD45.1 (A20, Biolegend), CD45.2 (104, Biolegend), CD62L (MEL-14, Biolegend), CD27 (LG.7F9, Biolegend), CD122 (TM-b1, eBioscience), CXCR3 (CXCR3-173, Biolegend), Bcl-2 (A19-3, BD PharMingen), Bcl-xL (H-5, Santa Cruz), Bcl-6 (K112-91, BD PharMingen), Eomes (Dan11mag, eBioscience), Ki-67 (16A8, BioLegend), Bim (C34C5, Cell Signaling Transduction), and MHC class I Dbgp33–41 tetramer (NIH tetramer core). Intracellular cytokine staining was performed after 5 hrs ex vivo stimulation with gp33–41 peptide in the presence of GolgiPlug (BD), GolgiStop (BD) and CD107a (1D4B, Biolegend). After stimulation, cells were stained with surface antibodies, following fixation with Fixation/Permeabilization Buffer (eBioscience) and then stained with intracellular antibodies for TNF (MP6-XT22, Biolegend), IFN-γ (XMG1.2, BD PharMingen), GrzmB (GRB17, Life Technologies) and MIP-1α (IC450P, R&D System) using Permeabilization Wash Buffer (eBioscience) according to manufacturer’s instructions. Cells were analyzed with LSRII (BD Biosciences) and FlowJo software (Treestar).
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6

Multi-parameter Flow Cytometric Analysis

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Single-cell suspensions from the indicated organs were treated with anti-CD16/32 (clone 93; Biolegend, San Diego, CA, USA) for Fc-blocking. The following antibodies were used for cell-surface staining: anti-B220 (RA3-6B2), CD19 (6D5); IgM (RMM-1); IgD (11-26c.2a); CD5 (53-7.3); CD21 (7E9); CD23 (B3B4), CD22 (OX-97); PIR-A/B (6C1); BAFFR (7H22-E16); CD3ε (145-2c11); CD4 (GK1.5); CD8α (53-6.7); CD11b (M1/70); Gr-1 (RB6-8c5); Ter-119 (TER-119); CD95 (Jo2); GL7 (GL7); CD138 (281-2); CD38 (90); IgG1 (RMG1-1); and Ki67 (16A8) (all from Biolegend). Anti-phospho-Btk (pY223: N35-86) and PLCγ2 (pY759: K86-689.37) antibodies were from BD Biosciences (San Jose, CA, USA). Debris and dead cells were excluded by forward scatter, side scatter and PI staining. All samples were analyzed by FACSCalibur or FACSAria (BD Biosciences). The data were analyzed using FlowJo (TreeStar, Ashland, OR, USA).
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7

Multiparametric Flow Cytometry Analysis of Immune Cell Subsets

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Mouse spleen and PLN were mechanically dissociated into single cells with use of 40-μm filters, and red cell lysis was performed with ACK buffer. Blocking was performed with anti-CD16/CD32 antibodies (BD Biosciences), and cells were stained with antibodies against CD4 (RM4-5; BD Biosciences), CD8 (53-6.7; BD Biosciences), CD11b (M1/70; BD Biosciences), CD11c (HL3; BD Biosciences), B220 (RA3-6B2; BD Biosciences), F4/80 (CI:A3-1; Bio-Rad Laboratories), CD62L (MEL-14; BD Biosciences), CD44 (IM7; BD Biosciences), CD25 (PC61; BD Biosciences), FoxP3 (FJK-16s; eBioscience), TIGIT (1G9; BioLegend), KLRG1 (2F1; BioLegend) and Ki67 (16A8; BioLegend). Samples were analyzed on the LSRII (BD Biosciences) and FlowJo (Tree Star, Inc.).
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8

Oncolytic Adenovirus and Anti-PD-1 Therapy

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Oncolytic adenovirus (OV) is a type 5 adenovirus with depleted E1b and E3 genes and a retained E1a gene. The human telomerase reverse transcriptase promoter was inserted upstream of the E1A gene to control virus replication. The OV was packaged and amplified in 293T cells, and ultracentrifugation was used for purification. Therapeutic anti-PD-1 antibodies were provided by Innovent Biologics (Suzhou, Jiangsu, China). Fluorescence-labeling antibodies to CD3 (17A2), CD4 (RM4-5), CD45 (30-F11), CD11b (M1/70), F4/80 (BM8), CD206 (C068C2), LAG-3 (C9B7W), PD-1 (RMP1-30), ICOS (7E.17G9), CD44 (IM7), CD62L (MEL-14), MHCII (M5/114.15.2), and Ki67 (16A8) were purchased from BioLegend, and antibodies to CD8 (53-6.7), FoxP3 (MF23), and IFN-γ (XMG1.2) were purchased from BD Bioscience. Antibody to adenovirus-5 E1A was purchased from Santa Cruz Biotechnology. OVA Tetramer-SIINFEKL-PE and fluorescein isothiocyanate-labeling anti-CD8 (KT15) were purchased from MBL.
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