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15 protocols using ic fixation and permeabilization buffer

1

Cytokine Detection in T. gondii Infection

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For cytokine detection, in vitro restimulation was performed for 20 h with 20 µg/ml of T. gondii lysate antigen in supplemented Iscove’s DMEM at 37°C with 5% CO2. Protein transport inhibitor (Thermo Fisher Scientific) and labeled anti-CD107a were added for the last 4 h of incubation. Following surface staining, cells were fixed and permeabilized using IC Fixation and Permeabilization buffer (Thermo Fisher Scientific) according to manufacturer’s instructions.
IL-21 staining was carried out using an rIL-21R/Fc fusion protein (R&D Systems) followed by PE-conjugated F(ab’)2 goat anti-human Fc (Jackson ImmunoResearch Laboratories) according to a previously published protocol (19 (link)).
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2

Comprehensive Flow Cytometric Analysis of Tumor Immune Microenvironment

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Cells were stained with fluorochrome-labeled anti-mouse Ab such as CD45, CD3, CD4, CD8, Foxp3, IFN-γ, IL-17A, CD11b, CD11c, pAKT, pSTAT3, CCR6, or MHCII. For intracellular cytokine staining, single-cell suspensions from the tumor and TDLNs were stimulated using a cell stimulation cocktail (eBioscience, San Diego, California, USA, 500X used at 1X) consisting of PMA (40.5 μM, Cayman, Ann Arbor, Michigan, USA), ionomycin (670 μM, BioVision, San Francisco, USA), and protein transport inhibitors-brefeldin A (5.3 mM, Thermo, Massachusetts, America) and monensin (1 mM, Thermo, Massachusetts, America) for 6 h at 37 °C and 5% CO2. After 6 h, the cells were harvested and washed, surface stained with CD45, CD3, CD4, CD8, CD11b, CD11c, CCR6, and MHCII (FACS Buffer, Thermo, Massachusetts, America), fixed, permeabilized (IC fixation and Permeabilization buffer, Thermo, Massachusetts, America), and stained for pAKT, pSTAT3, IFN-γ, and IL-17A (Thermo, Massachusetts, America). Isotype controls with the same fluorochrome were used as controls. Cells were acquired using the FACS Aria II machine and analyzed using FlowJo software.
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3

Comprehensive Flow Cytometry Immunophenotyping

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Cells were stained using Abs specific for mouse Ags: CD45R (B220) (various fluorochromes) (BD Pharmingen, BioLegend, San Diego, CA and Tonbo Biosciences); IgM (various fluorochromes, Jackson ImmuoResearch Laboratories, West Grove, PA); CD19 eFlour450, CD25 APC, MHC II APC (Tonbo Biosciences); CD43 PE, BP-1 PE, CD117 PE, CD24 (HSA) PE-Cy7, IgD FITC (BD Pharmingen); CD21 PerCP/Cy5.5 (BioLegend). IC staining was performed with IC fixation and permeabilization buffer (eBiosciences). Methanol fixation was performed for IC phospho (p)-S6R detection. Abs used for IC staining were p-ribosomal S6 protein (S6R) S235/236 PE (eBiosciences); p-AMPKα T172, c-Myc AF488 and p-Ulk1 S555 (Cell Signaling Technology, Danvers, MA). Donkey anti-rabbit Alexa-Fluor 647 (Life Technologies, Carlsbad CA) secondary Ab was used to detect unlabeled primary Abs. Data was collected using FACS Canto II or LSR II flow cytometers (BD Biosciences) and analyses were performed using FlowJo software (TreeStar, Ashland, OR).
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4

Intracellular IL-21 in KRN.g7 Mice

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Cells from the joint draining LNs of 6 week old KRN.g7 and IDO2 ko KRN.g7 mice were harvested and cultured for 4 hours with 50 ng/ml PMA, 500 ng/ml ionomycin, and 3 μg/ml brefeldin A. After 4 hours, cells were harvested, surface stained for CD4 and CD8 (eBioscience), fixed and permeabilized (IC Fixation and Permeabilization Buffer, eBioscience), then stained for intracellular IL-21 or isotype control. The samples were acquired on a BDFACSCanto II flow cytometer using FACSDiva software and analyzed with FlowJo software.
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5

Multiparametric Flow Cytometry of PBMCs

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Freshly thawed or CMV-stimulated PBMC were washed in staining medium and incubated for 30 min at 4°C with surface markers. For intracellular Granzyme B, TGFβ, IL-35 and IL-10 staining, PBMC were then permeabilized and fixed (Cytofix/Cytoperm; BD Biosciences) for 20 min at 4°C, washed and incubated with the appropriate mAbs. For intranuclear FoxP3, cells were permeabilized and fixed with IC Fixation and permeabilization buffer (eBiosciences) for 1 hour at 4°C, washed and incubated with the mAb. At the completion of the staining procedure, cells were fixed in 2% paraformaldehyde (Electron Microscopy Sciences) in PBS and data were acquired with Guava 8HT (Millipore) or Gallios (Beckman Coulter). Results were analyzed with FlowJo (Treestar) or Kaluza (Beckman Coulter).
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6

Flow Cytometry Staining of PBMCs

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PBMCs were washed in flow buffer (PBS containing 0.2% BSA and 5 mM EDTA), passed through a cell strainer (40-μm pore, Corning) to remove aggregates, and plated at 5 × 105 cells per well in 96-well conical bottom plates (Nunc) on ice. Cells were treated with human FcR blocking reagent (Miltenyi Biotec) and DAPI (4′,6-Diamidino-2-Phenylindole, Dihydrochloride, Invitrogen) or Zombie Violet™ (Biolegend) for 15 min on ice and then washed three times in flow buffer prior to antibody labeling. Cell surface molecules were stained with antibodies (Supplementary Table 1) for 20 min on ice, washed twice in flow buffer, and resuspended in 2% formalin (0.2 ml). Cells for intracellular (IC) staining were treated with IC fixation and permeabilization buffer (eBioscience) prior to staining. Cells were stained with IC antibodies (Supplementary Table 1) in IC fixation and permeabilization buffer for 20 min at room temperature. Cells were washed in flow buffer then transferred to 96-well Micronics plates for analysis.
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7

Intracellular IL-21 Expression Analysis

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Cells from the joint draining LNs of 6 week old control or IDO2 Ig-treated KRN.g7 mice were harvested and cultured for 4 hours with 50 ng/ml PMA, 500 ng/ml ionomycin, and 3 μg/ml Brefeldin A. After 4 hours, cells were harvested, surface stained for CD4 and CD8 (eBioscience), fixed and permeabilized (IC Fixation and Permeabilization Buffer, eBioscience), then stained for intracellular IL-21 or isotype control. The samples were acquired on a BDFACSCanto II flow cytometer using FACSDiva software and analyzed with FlowJo software.
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8

Intracellular IL-21 Quantification in KRN.g7 Mice

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Cells from the joint draining LNs of 6 week old KRN.g7, IDO1 ko KRN.g7, IDO2 ko KRN.g7, and dko KRN.g7 mice were harvested and cultured for 4 h with 50 ng/ml PMA, 500 ng/ml ionomycin, and 3 μg/ml brefeldin A. After 4 h, cells were harvested, surface stained for CD4 (eBioscience), fixed and permeabilized (IC Fixation and Permeabilization Buffer, eBioscience), then stained for intracellular IL-21 (eBioscience). The samples were acquired on a BD FACSCanto II flow cytometer using FACSDiva software and analyzed with FlowJo software.
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9

Flow Cytometry Analysis of Activated Lymphocytes

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Lymphocytes 5 × 106 in 1 mL culture medium were stimulated with 1 µg/mL PepMix a for 2 h and then for an additional 12 h in the presence of 1:1000 diluted Golgi plug (BD Biosciences, Franklin Lakes, NJ, USA). After incubation, cells were harvested, washed with PBS and stained with the LIVE/DEAD Blue Dead Cell Staining Kit (Thermo Fisher) and with antibodies to CD56-BV510 (Biolegend, San Diego, CA, USA), CD8-AlexaFluor700 (Exbio, Prague, Czech Republic). CD45RO-BV786, and CCR7-BV605 (BD Horizon, BD Biosciences). The cells were then washed with PBS, fixed using IC Fixation and Permeabilization Buffer (eBioscience, San Diego, CA, USA) for 20 min and stained intracellularly with antibodies against IFN-gamma-PE, CD3-APC-Cy7 (Biolegend, San Diego, CA, USA), and CD4-PacificBlue (Exbio) in a the permeabilization buffer. The cells were washed and resuspended in a FACS buffer (FB-PBS containing 0.09% sodium azide, 1% BSA) and measured using the BD LSR Fortessa 5 L flow cytometer (BD Biosciences). The obtained data were analysed by the FlowJo 10.5 software (TreeStar, Ashland, OR, USA). The gating strategy is shown in suplementary Fig. S 2.
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10

Single Cell Suspension Preparation and Cytokine Analysis

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Single cell suspensions were prepared from the indicated tissues as previously reported6 (link). Data were acquired on LSR Fortessa or LSRII flow cytometers (BD Biosciences) and analyzed using FlowJo v9.3 (FlowJo) or software designed by the Division of Computer Research and Technology, NCI. Live cells were gated using forward scatter exclusion of dead cells stained with propidium iodide. For fixed cells, dead cells were excluded by Aqua Live/Dead (Invitrogen) staining and fixation and permeabilization were performed with IC fixation and permeabilization buffers (eBioscience). Cytokine expression was assessed on cells upon stimulated in vitro with PMA (25 ng/ml) and ionomycin (1 μM) for 4 hours as previously described53 (link).
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