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8 protocols using efluor 520

1

Optimized Liver FNA Immunophenotyping

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Preparation of liver FNAs was optimized to minimize cell loss. Longitudinal liver FNAs and matched PBMCs from the same patients were thawed. Dead cells were stained with eFluor 520 (eBioscience). An equal volume of 2× concentrated extracellular antibodies was added. Further information on antibodies used is listed in Supplemental Table 3. Cells were washed and fixed for flow cytometry analysis. Data were analyzed with FlowJo, version 10.7.1.
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2

Isolation and Analysis of Murine Lung Immune Cells

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Mice were euthanized by intraperitoneal administration of pentobarbital at the indicated time points. Lungs were isolated in HBSS buffer (Sigma, St. Louis, MO), digested with type IV collagenase (Worthington Biochemical, Lakewood, NJ) for 30 min with agitation, and then processed into single-cell suspensions by forcing the digested lungs through a 70-µm nylon cell strainer (Falcon, Corning, NY). Single-cell suspensions were stained in PBS supplemented with 1% bovine serum albumin and 2 mM EDTA. Antibodies against the following immune markers were used for discrimination of immune cell types: CD45 (30-F11; BD), CD11b (M1/70; BioLegend), CD11c (HL3; BD), Ly6c (HK1.4; eBioscience), GR1 (RB6-8C5; eBioscience), major histocompatibility complex class II (MHCII) (M5/114.15.2; BD), and SiglecF (E50-2440; BD). Live cells were discriminated from dead cells by using a viability dye eFluor 520 (eBioscience). All flow cytometry data were acquired on an LSR-II flow cytometer (BD) and analyzed using FlowJo software (FlowJo LCC, Ashland, OR). Cell sorting was performed on a FACS Aria (BD).
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3

Single-Cell Flow Cytometry with Intracellular Staining

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The single‐cell suspension was blocked with mouse FcR blocking (Miltenyi Biotec) prior to surface staining. Fixable viability dye eFluor 520 (eBioscience) was used to exclude dead cells. For intracellular staining in T cells, after ex vivo stimulation with the leukocyte activation cocktail (BD Biosciences) for 5 hours, cells were fixed and permeabilized by using a fixation/permeabilization kit (BD Biosciences) followed by intracellular cellular staining after staining with surface antibodies. Data were acquired on BD FACS Calibur and analyzed by Flow‐Jo.
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4

Multiparameter Flow Cytometry Panel

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A single-cell suspension was blocked with mouse FcR blocking reagent (Miltenyi Biotec, USA) at 4°C for 10 min prior to surface staining. For intracellular IFN-γ staining, the cells were fixed and permeabilized with Fixation/Permeabilization Kit (BD Biosciences, USA) and then stained with IFN-γ antibody. The following anti-mouse antibodies were used: PE-CD44 (clone:IM7), APC-CD24 (clone:M1-69), FITC-CD3e (clone: 145-2C11), PE-CD45 (clone:30-F11), APC-MHC class II (I-A/I-E) (clone: AMS-32.1), PE-CD86 (clone: GL 1) from eBioscience (San Diego, CA, USA); PE/Cy7-CD8a (clone: 53-6.7), PE-MHC class I (H-2Kd) (clone: AMS-32.1), PE/Cy7-CD40 (clone: 3-23), PE/Cy7-CD11c (clone: HL3) from BD Biosciences (USA); and APC-CD8a (clone: 53-6.7), PE-IFN-γ (clone: XMG 1.2), APC-CD11c (clone:N418), APC-CD80 (clone: 16-10A1) from Biolegend (USA). For ALDH1 staining, the ALDH1 activity was detected by the ALDEFLUOR kit (Stem Cell Technologies, Canada) according to the instructions of the manufacturer. Data were acquired on BD FACS Calibur (USA) and analyzed by the Flow-Jo software (Tree Star, OR) version 7.1.2. Fixable viability dye eFluor 520 (eBioscience, USA) was used to exclude dead cells.
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5

Multicolor Flow Cytometry for Bone Marrow and Spleen Progenitors

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For assessment of bone marrow and spleen progenitor cells by flow cytometry, single-cell suspensions of freshly prepared bone marrow and spleen were incubated with the following anti-mouse monoclonal antibodies: Ter119 (Ly-76, BD Biosciences), CD71 (C2, BD Biosciences), CD34 (RAM34, BD Biosciences), CD135 (A2F10, eBioscience), CD127 (A7R34, eBioscience), c-Kit (ACK2, eBioscience), SCA-1 (LY-6A/E, BD Biosciences), eFluor520 (eBioscience), and 7-AAD (eBioscience). Lineage (lin) staining included anti-mouse Ter119 (BD Biosciences), GR-1 (RB6-8C5, BD Biosciences), B220 (RA3-6B2, BD Biosciences), CD4 (RM4-5, BD Biosciences), CD8 (53–6.7, BD Biosciences), and CD11b (M1/70, BD Biosciences) antibodies [22 (link)–24 (link)]. Multicolor data acquisition for bone marrow progenitor subsets was performed on a FACSCanto II flow cytometer, and data were analyzed with FlowJo 7.6.1.
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6

Cell Surface Protein Staining

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Prior to cell staining, primary cells were quickly thawed in a water bath at 37 °C and collected by centrifugation, while cells from cultured cell lines were harvested by Trypsin–EDTA digestion. All cells were rinsed twice with cold PBS prior to antibody staining. All the following steps were carried out at 4 °C. The cell pellet was washed twice with PBS and incubated with a viability dye eFluor 520 (eBioscience) in PBS for 30 min. After washing twice with cold PBS, 1/3 of the cells were saved as unstained control. The rest of the cells were split into two tubes and incubated with 5 μg/mL Alexa Fluor 647-conjugated G10C or isotype control (see the Supporting Information for preparation of the conjugates) in 5% BSA in PBS for 1 h. The stained cells were washed twice with 5% BSA in PBS and resuspended in 0.3 mL of buffer. Flow analysis was performed using a BD FACS Calibur cell analyzer. Dead cells were excluded from analysis using the eFluor 520 viability dye as these cells gave a false-positive result presumably due to G10C staining of intracellular proteins.
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7

OVA-specific CD8+ T Cell Activation Assay

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CD8+ T cells from spleen of OT-I mice were enriched using a naïve mouse CD8+ T cell isolation kit (Miltenyi Biotec). Enriched CD8+ T cells were labelled with CTV according to the manufacturer’s protocol. MACS-sorted reprogrammed cells, non-reprogrammed cancer cells, eGFP transduced cancer cells and CD103+ BM-DCs were incubated at 37 °C with OVA peptide (SIINFEKL, T cell priming assays) or protein (cross-presentation assays). OVA expressing cells were not incubated with exogenous OVA. Cells were incubated overnight in the presence of Poly(I:C) or IFN-γ where indicated. 5x103 antigen presenting cells were incubated with 1x105CTV-labelled OT-I CD8+ T cells in 96-well round-bottom untreated-tissue culture plates. After 3-days of co-culture, T cells were collected, stained for viability (fixable viability dye eFluor-520, eBioscience), CD8α, TCR-β, and CD44 and analyzed by flow cytometry. T cell proliferation (dilution of CTV) and activation (CD44 expression) were determined by gating on live, single, TCR-β+ and CD8+ T cells. The threshold for data plotting was fixed at 1,000 events within live cell gating.
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8

Microglial Isolation from Murine Brain

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Brains were dissected into 1-2 mm 3 pieces with small scissors and incubated for 30 min at 37°C in 1 ml HBSS solution containing 2% FBS, 1 mg/ml Collagenase D and 50 µg/ml DNase I. 10 mM EDTA was added to the 1.5 mL tube to stop the enzymatic reaction and homogenates were pipetted for further dissociation. Next the homogenates were ltered through a nylon mesh (70 µm pore size) in a 50 mL tube using the plunger of a 10 mL syringe, washed with cold FACS buffer (2% FBS, 1 mM EDTA in PBS without Ca 2+ or Mg 2+ ) and centrifuged at 300g at room temperature for 5 min. For the enrichment of microglia, the cell pellet was resuspended with 30%-37%-70% Percoll density gradient medium and centrifuged at 800g, no acceleration and braking, at room temperature for 40 min. Next, the 70-37% density gradient interphase containing the macrophage subpopulations cells was collected into a clean tube, washed with 5 ml FACS buffer and centrifuged at 500g at 4°C for 5 min, followed by antibody labeling and ow cytometry analysis. Antibodies against PerCP-CD11b (Biolegend, San Diego, CA), PE-CD45 (Biolegend, San Diego, CA), CD16/32 (Biolegend, San Diego, CA), xable viability dye eFluor 520 (ebioscience, San Diego, CA) were used. Analysis was performed on a Calibur (BD Biosciences, BD Diva Software) and analyzed with FlowJo software.
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