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22 protocols using gr 1 fitc

1

Multicolor Flow Cytometry Analysis of Immune Cells

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Cell suspensions from SPL, mLN, and cLP were analyzed by flow cytometry. Conventional CD4+ T cells and Tregs were stained with anti-CD3ε and anti-CD4 mAbs (BD Biosciences, San Jose, CA) and intracytoplasmic anti-foxp3 mAbs (eBioscience, San Diego, CA). Neutrophils were stained with Gr-1-FITC, CD11b-PECy7, and Ly6G-AF647 mAbs (eBioscience). Plasmacytoid dendritic cells (pDCs) and conventional dendritic cells (cDCs) were stained with MHCII-FITC, CD11b-PECy7, PDCA-1-AF647, and CD11c-APCCy7 mAbs with a lineage-negative mAb cocktail containing B220-biotin, CD3ε-biotin, Ly6G-biotin (eBioscience) and PerCP-Cy5.5-conjugated streptavidin. The cDC subsets were stained with MHCII-FITC, CD11c-APCCy7, CD11b-PECy7, and CD103-PE mAbs with a lineage-negative mAb cocktail containing B220-biotin, CD3ε-biotin, Ly6G-biotin (eBioscience) and PerCP-Cy5.5-conjugated streptavidin (eBioscience). Monocytes and macrophages (MΦ) were stained with Gr-1-FITC, MHCII-PE, Ly6C-PerCP-Cy5.5, CD11b-PECy7, Ly6G-APC, and CD11c-APCCy7 mAbs (eBioscience). Blocking of FcγR binding was performed using mouse and rat serum (Jackson ImmunoResearch, West Grove, PA). Cells were analyzed on a FACS Canto II (BD Biosciences). Data were collected using FACS Diva software (BD Biosciences) and analyzed with FlowJo software (TreeStar, Ashland, OR).
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2

Tumor and Lymph Node Immune Profiling

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Tumor and lymph node immune infiltrates were evaluated on Day 5 post therapy. Injected tumors, contralateral tumors and draining lymph nodes were harvested and single-cell suspensions surface stained with CD3-APC, CD4-FITC, CD8-PE-Cy7, IFNγ-PE, CD11b-PE, CD11c-APC-Cy7, CD44-APC, CD62L-PE (BD), Foxp3-APC and Gr-1-FITC (eBioscience, San Diego, CA) and fixed using BD Cytofix/Cytoperm.
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3

Cytokine Expression Profiling of Hepatic Immune Cells

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Single cell suspensions were derived from hepatic homogenate and stained with directly conjugated monoclonal antibodies or isotype controls. Staining for cytokine expression was completed after 4 hours of stimulation with 50 ng/mL Phorbol 12-Myristate 13-acetate (PMA; Promega), 1 μg/mL Ionomycin (Calbiochem) and 10μg/mL Brefeldin A (Gold Bio). Data collection and analysis were done as previously described11 (link),63 (link). Briefly, cells were stained with Live/Dead stain (Zombie UV Dye: Biolegend) and with directly-conjugated monoclonal antibodies to CD45-AF700 (104), CD11b-PE (M1/70), F4/80-APCef780 (BM8), Ly6C-Percp (HK1.4), Gr1-FITC (RB6-8C5), NK1.1-PECy7 (PK136), TCRβ-PE (H57-597), CD4-APCef780 (GK1.5), CD8-ef450 (53-6.7), TNF-BV650 (MP6-XT22), IL-17A-Percp (17B7) and IL-17F-PE (18F10) [all antibodies from e-Bioscience]. Flow cytometry data were then collected using a LSR Fortessa (BD) flow cytometer and analyzed using FlowJo X software (vX0.7).
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4

Comprehensive Hematopoietic Cell Analysis Protocol

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Flow assisted cell sorting (FACS) was performed as described elsewhere (16 (link)) with the following conjugated antibodies; Mac1 PE, Gr1 FITC, B220 APC, B220 FITC, CD19 PE, surface IgM PE, CD43 FITC, CD3 PE, CD4 APC, CD8 FITC, CD71 PE, Ter119 FITC, Sca-1 PE, cKit FITC, cKit APC-Cy7, IL7Ra PECy7, CD34 FITC, CD16/32 PE (eBiosciences or BD Biosciences). StemSep Mouse Hematopoietic Progenitor Kit Lineage Positive antibody cocktail (Stem Cell Technologies, Vancouver, Canada) was used to detect lineage positive bone marrow cells, stained as previously described (16 (link)). Apoptosis assays were conducted using AnnexinV-FITC Apoptosis Detection Kit I following the manufacturer’s recommended protocol. IHC and immunoblotting were performed as previously described (49 (link)). Formalin-fixed paraffin embedded sections were stained with hematoxylin and eosin (H&E), myeloperoxidase (MPO) (A0398, DAKO), CD3 (MCA1477, AbD Serotec), B220 (553086, BD), Ter119 (116201, BioLegend). Stained slides were scanned and imaged as described elsewhere (49 (link)). For immunoblots, primary antibodies used were anti-V5 (ab9116, Abcam or R960-25, Life Technologies), and beta-actin (Cell Signaling Technology). Protein was visualized using Pierce ECL Western Blotting Substrate (Thermo Scientific, Illinois, USA) and Amersham Hyperfilm ECL (GE Healthcare Ltd, Buckinghamshire, UK).
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5

Isolation and Characterization of Tumor-associated MDSC

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BALB/c mice were inoculated in the abdominal mammary gland with 4T1 or 4T1/IL1β tumor cells, and MDSC were harvested from the mice as described by Chornoguz et al. [9 ]. Briefly, mice with primary 4T1 or 4T1/IL1β tumors of ~7–10 mm in diameter and established metastatic disease were bled from the submandibular vein into heparinized tubes. Red blood cells were removed by lysis and the remaining leukocytes were used immediately or frozen at –80C until used. The percent of MDSC in the ex vivo leukocyte population was determined by immunofluorescence and flow cytometry using the fluorescent antibodies Gr1-FITC and CD11b-PE (eBioscience, Inc., San Diego, CA) as described [9 ]. Individual biological samples consisted of MDSC pooled from two to three individual mice and consisted of >90% Gr1+ CD11b+ cells (see Fig. 1A).
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6

Immune Signaling Pathway Analysis

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Lipopolysaccharide (LPS, Escherichia coli 0111:B4), lipoteichoic acid (LTA), and polyinosinic:polycytidylic acid (Poly I:C) were from Sigma-Aldrich, and phosphorothioate-modified CpG ODN was synthesized by Sybersyn. Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (197G2) rabbit mAb, Phospho-SAPK/JNK (Thr183/Tyr185) (81e11) rabbit mAb, Phospho-p38 MAPK (Thr180/Tyr182) (D3F9) rabbit mAb, Phospho-NF-κB p65 (Ser536) (93H1) rabbit mAb, EEA1 (C45B10) rabbit mAb, Rab5 (C8B1) rabbit mAb, and Rab7 (D95F2) rabbit mAb were from Cell Signaling Technology. CD107a/LAMP-1 mouse mAb was from BioLegend; β-actin mouse mAb and Ccz1 antibodies (L-20) were obtained from Santa Cruz Biotechnology; SNX10 antibody (HPA015605) was acquired from Sigma-Aldrich. Mouse CD4-FITC, CD8-PE, B220-APC, CD11b-PE, CD11b-APC, Gr1-FITC, Ly6C-PE, and F4/80-APC antibodies were purchased from eBioscience. Fluorescein isothiocyanate isomer I (FITC) and Cell Counting Kit-8 (CCK-8) were from Sigma-Aldrich; Alexa Fluor® 488 dye and Alexa Fluor® 647 dyes were from Thermo Fisher Scientific.
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7

Multi-Marker Immune Cell Profiling

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Tumor-infiltrating immune cells were incubated with Fc-blocking reagent (anti CD16/CD32, BD Biosciences), followed by CD11b-APC (M1/70, BD Biosciences), Gr1-FITC (RB6–8C5, BD Biosciences), CD11c-APC (HL3, BD Biosciences), MHC II-FITC (I-Ab, AF6–120.1, BD Biosciences), CD3 -APC (145–2C11, eBioscience), CD4-FITC (GK1.5, eBioscience), CD8a-APC (53–6.7, eBioscience) along with isotype-matched control. In vitro cultures dendritic cells (DCs) were stained with CD11b-APC, Gr1-FITC, CD11c-APC, MHC II-FITC, CD80-FITC (16–10A1, eBioscience) and CD86-FITC (GL1, eBioscience).
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8

Flow Cytometry Analysis of Immune Cells

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Cell suspensions were subjected to flow cytometry analyses61 (link). For gating strategy, first FSC/SSC was applied to gate the live cells and then according to fluorochrome to make the subsequent gates. All the samples in the same experiments and comparisons were gated under the same parameters. The antibodies used in this study were as follows: anti-CD11b-APC, eBioscience, Cat# 47-0112-82 (1:400); anti-F4/80-PE, eBioscience, Cat# 25-4801-82 (1:400); anti-CD4-FITC, eBioscience, Cat# 11-5040-41 (1:400); Gr-1-FITC, eBioscience, Cat# 11-0114-82 (1:400).
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9

Multiparametric Immune Cell Analysis

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Fluorescence-conjugated anti-mouse CD45 allophycocyanin (APC), phycoerythrin(PE) Cy7, Brilliant Violet™ 421, CD3 FITC, B220 PE, APC, Brilliant Violet™ 711, CD19 FITC, PE, APC, IgM FITC, PECy7, APC, IgD PE, CD21 FITC, CD23 PE, CD24 PECy7, CD43 PE, CD5 PECy7, CD62L FITC, GL-7 APC, CD93 APC, LFA-1 PE, VLA-4 APC, CXCR4 APC, CXCR5 APC, CD35 FITC and IL-7R APC, CD4 FITC, CD8 FITC, CD11b FITC, Gr-1 FITC, NK1.1 FITC, TER119 FITC (e-bioscience or BioLegend), anti-ALCAM (R&D Systems), anti-Rap1 (BD Biosciences), Extracellular signal-regulated kinase (ERK), p-ERK, Akt kinase (Akt), p-Akt, β-actin and peroxidase-conjugated goat anti-mouse IgG (Cell Signaling) were used for flow cytometry, immunostaining and immunoblotting. Mouse CXCL13, CXCL12 and 7α,25-OHC were purchased from R&D Systems and Sigma. NIP-APC (4-hydroxy-3-iodo-5- nitrophenylacetate-allophycocyanin) was generated in-house (34 (link)).
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10

Comprehensive Antibody Validation for Diverse Assays

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Antibodies used for western blots (all diluted by 1:2000) include anti-Flag (M2)-HRP (Sigma, A8592), anti-H3 (CST, 9715), anti-GAPDH (CST, 2118), anti-β-Tubulin (CST, 2146), Streptavidin-HRP (CST, 3999) and anti-GFP (CST, 2956). Antibodies used for FACS (all diluted by 1:100) include c-KitAPC (Invitrogen, 17-1172-82), c-KitFITC (eBioscience,11-1171-85), Cd34APC (eBioscience, 50-0341-82), Cd34FITC (BD, 560238), Mac1APC (BD, 557686), Mac1FITC (eBioscience, 11-0112-85), Gr1FITC (eBioscience, 11-5931-85), Cd4FITC (eBioscience,11-0042-82), Cd8aFITC (eBioscience,11-0081-82), and Cd19FITC (eBioscience,11-0193-82). Antibodies used in ChIP, ChIP-seq and CUT&RUN assays include anti-Flag (Sigma, F1804), anti-HA (Abcam, ab9110), anti-GFP (Abcam, ab290), anti‐H3K36me3 (Abcam, ab9050), anti-H3K27ac (Abcam, ab4729), anti‐H3K27me3 (Millipore, 07-449), anti-H4ac (Millipore, 06-866), anti-BRD4 (Bethyl, A301-985A100) and anti-Tip60 (Santa Cruz, sc-166323). 10 ug antibodies were mixed with 100 μl Dynabeads for each ChIP or ChIP-seq assay. All antibodies used in CUT&RUN assays were diluted by 1:100.
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