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8 protocols using fix perm cell fixation and cell permeabilization kit

1

Characterization of Canine CTLA4 Expression

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MDCK, MDCK-FcγRI and MDCK-CTLA4 cells were trypsinized and washed with FACS buffer (1× PBS containing 1% bovine serum albumin (BSA), 2 mM EDTA, 0.02% sodium azide, and HEPES). Cells were incubated in blocking buffer (PBS containing 4% goat or rabbit serum, 1% BSA, 0.02% sodium azide) and stained with anti-CTLA4 Nbs and cHcAbs. Bound Nbs or cHcAbs were detected by using anti-His 647 or anti-canine IgG Fc 647 or 750 secondary antibodies and analyzed by flow cytometry. Canine PBMC were cultured overnight in RPMI media. PBMCs were stimulated with various concentrations (50, 100 and 150 ng/mL) of PMA and Ionomycin (1 µM/mL final concentration) for 6 h. Stimulated PBMCs were blocked and stained with anti-CTLA4 Nbs and cHcAbs. Cells were also stained with anti-CD3FITC (clone CA17.2A12), anti-CD4RPE (clone YKIX 302.9), and anti-CD8 647 (clone YCATE55.9) antibodies to characterize subpopulations expressing canine CTLA4. For intracellular FOXP3 staining, cells were fixed and permeabilized using the fix & perm cell fixation and cell permeabilization kit from Life Technologies and stained with FOXP3 monoclonal antibody (FJK-16s [ThermoFisher]).
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2

Analyzing Ryanodine Receptor and Rab23 Levels

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After 48 h of cellular transfection, cells were permeabilized with the FIX & PERM Cell Fixation and Cell Permeabilization Kit (Life Technologies) and incubated with anti-RYR3 antibody (NPB1-70399; Novus Biologicals, Littleton, CO). The amount of RYR3+ cells was estimated by flow cytometry in the Guava easyCyte 5HT Flow Cytometer (Millipore, Billerica, MA). RAB23 protein levels were analyzed by western blotting under standard conditions. After protein transfer, PVDF membranes (GE Healthcare, Little Chalfont, UK) were blocked, incubated first with anti-RAB23 antibody (ABcam Cat. No.169491) and then with a goat anti-mouse HRP-conjugated secondary antibody. Protein bands were revealed using the Immobilon Western Chemiluminescent HRP Substrate (Millipore).
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3

Lactobacillus Colonization of Tonsillar Tissue

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Tonsillar tissues were colonized with 15 vaginal Lactobacillus strains (27 blocks per condition) at a starting inoculum of 104 CFU/mL. At day 3 after inoculation with bacteria, all tissue blocks were collected and digested with collagenase IV (5 mg/mL; Gibco BRL) for 30 min with agitation in a Thermomixer at 900 rpm at 37°C. Following digestion, tissue cells were filtered with 100 μm cell strainers (Corning) and washed with 50 mL of PBS. Cells were then suspended in 1 mL of PBS and stained with 1 μl of live/dead Fixable Viability Dye eFluor 450 (EF 450, Invitrogen) for 15 min. After incubation, cells were washed and diluted in staining buffer [PBS, 1% normal mouse serum, 1% normal goat serum, 1 mM ethylenediaminetetraacetic acid (EDTA)] and stained with anti-CD3-allophycocyanin (CD3-APC) for 20 min. After surface staining, cells were permeabilized with the Fix&Perm Cell Fixation and Cell Permeabilization Kit (Invitrogen) then stained for 20 min with anti-Bcl2-PE, a mitochondrial anti-apoptotic antigen. Data were acquired with a Novocyte flow cytometer (ACEA Biosciences, CA, United States) equipped with 405, 488, and 640 nm laser lines using NovoExpress version 1.2.4 software (ACEA Biosciences) and analyzed using the same software.
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4

Evaluating Endolysosomal Network by Flow Cytometry

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We performed tests on the endo-lysosomal network by CD63 and CD107a staining, using anti-CD63 and anti-CD107a antibodies which are respectively endosome and lysosome markers [77 (link)]. Using flow cytometry, we can measure the intracellular content of these two molecules with previous cellular fixation and permeabilization (FIX & PERM® cell fixation and cell permeabilization kit—Invitrogen) [78 (link)]. Niemann-Pick and wild-type B lymphocytes were washed in PBS, resuspended in 250μl of FIX reagent and incubated at 4°C for 30 min. Then the cells were washed in the perm/washing buffer and resuspended in 250μl of PERM reagent. Mouse monoclonal anti-Human Antibodies anti-CD63 (clone TEA3/18, Immunostep) and anti-CD107a (clone H4A3, BioLegend), FITC- and PerCP/Cy5.5-conjugated respectively, were added to the bottom of the tube and incubated at 4°C for 30 min, at concentrations indicated in the manufacturer’s instructions. After a washing step, the supernatant was discarded and samples were acquired by flow cytometry, collecting at least 10,000 events for each tube.
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5

Retinal Cell Isolation and Characterization

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Retinas were isolated and digested immediately with collagenase I (100 U/ml, Biochrom, Berlin, Germany) in DMEM/F12 medium for 30 minutes at 37°C. The reaction was stopped by the addition of DMEM with 10% FCS and the tissue was further dissociated by gentle trituration using a sterile Pasteur pipette [24 (link)]. Cells were fixed and permeabilized by using FIX & PERM cell fixation and cell permeabilization kit (Invitrogen) according to the standard protocol. Antibodies directed against Cyp2c44 and AQP-4 were used at 1:200 and 1:500 dilution, respectively.
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6

Multicolor Flow Cytometry Immunophenotyping

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Cells were blocked in Fc Receptor Binding Inhibitor Monoclonal Antibody and incubated with LIVE/DEAD Fixable Dead Cell Stain (Thermo Fisher Scientific). Cells were stained using the FIX & PERM Cell Fixation and Cell Permeabilization Kit (Thermo Fisher Scientific). For the immunophenotyping, 100 µl blood was incubated with appropriate antibodies for 30 min at room temperature. Red cell lysis was performed with FACS Lysing Solution (BD Biosciences) according to the manufacturer’s recommendations. Samples were run on the BD FACSCanto II, and data were acquired using BD FACSDIVA software (BD Biosciences). Data were analyzed using FlowJo.
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7

Phospho-flow and Cell Cycle Analysis of Hematopoietic Stem and Progenitor Cells

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For phospho-flow analysis, sorted LSKs from experimental mice (Mx1-Cre or ERT2-Cre) were stimulated with increasing concentrations of Ifnα, Ifnγ, Il3, Il6, or G-Csf for 15 min at 37°C, fixed with formaldehyde, and permeabilized by adding cold 100% methanol slowly to pre-chilled cells, while vortexing. Cells were then stained for 30 min at RT in the dark with phospho-specific antibodies or isotype controls. For cell cycle analysis, BM cells were first surface stained to identify LSKs followed by mild fixation and permeabilization of cells using the FIX & PERM Cell Fixation and Cell Permeabilization Kit (Thermo Fisher Scientific) following the manufacturer’s recommendations. Ki67-FITC (eBiosciences) was added to the Medium B prior to permeabilization of the cells. DAPI was used as counterstain. Cell cycle analysis under homeostasis was performed at least 4 weeks post completion of poly(I:C) injections.
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8

Whole-Blood TNF-α Production Assay

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A whole-blood stimulation assay was used to evaluate TNF-α production. Five hundred microliters of blood were mixed with 500 µL of RPMI culture medium from Gibco 1640 (Thermo Fisher Scientific, Waltham, MA), and incubated at 37°C and 5% CO 2 . The culture medium was supplemented with IL-6 (100 ng/mL) and brefeldin A (BioLegend) (5 μg/mL); with LPS from Escherichia coli O111:B4 (Sigma Aldrich, St. Louis, MO) (250 ng/mL) and brefeldin A (5 μg/mL); or with IL-6 (100 ng/mL), followed by LPS (250 ng/mL) and brefeldin A (5 μg/mL). After the indicated incubation times, the following antibodies were added: anti-CD45/Pacific Blue (BioLegend, clone J.33), anti-CD14/PE-Cy7 (BioLegend, clone MSE2) and anti-CD16/APC-Cy7 (BioLegend, clone 3G8). After 15 min, 50 µL of Buffer A of the Fix & Perm cell fixation and cell permeabilization kit (Thermo Fisher Scientific) were added. After 20 min, 1 mL of PBS was added, and the cells were centrifuged at 350 xg for 5 min. The cells were resuspended in 50 µL of Buffer B that contained anti-TNF-α/PE antibody (BioLegend, clone MAb11) and incubated for 30 min. The cells were washed with 1 mL of PBS and acquired in a FACSAria flow cytometer (BD Biosciences). Data was analysed with Infinicyt software (Cytognos).
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