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26 protocols using cell fix solution

1

Characterizing TIL Phenotypes in HCC

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The generated short-term T cell lines were stimulated with mixed TAAs for 4 hours and cells without stimulation were used as negative controls. Then, cells were stained with LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific) and surface markers, including CD3-AF700 (Bio Legend), CD4-FITC (BD Biosciences), CD8-APC-H7 (BD Biosciences), PD1-BV650 (BD Biosciences), and Tim3-BV421 (Bio Legend), fixed with 1 × CellFix solution (BD Biosciences) and acquired immediately on a BD LSR Fortessa. Fluorescence minus one (FMO) controls were applied accordingly in order to properly position gates.
In the validation cohort, 60 samples from 26 HCC patients were thawed and rested overnight. These cells were stained with LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific) and surface markers, including CD3-BV786 (Bio Legend), CD4-BV711 (Bio Legend), CD8-Percp-cy5.5 (BD Biosciences), and CD39-PE-CF594 (Bio Legend), fixed with 1 × CellFix solution (BD Biosciences), and acquired immediately on a BD LSR Fortessa. Flow data were analyzed by FlowJo V.10.0.
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2

Monocyte Subpopulations Analysis by Imaging Flow Cytometry

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Cells were stained as described for flow cytometry analysis (Table 2, combination E) without viability staining. Cells were finally fixed in 50 μL of BD CellFIX solution (BD Biosciences) and nuclei were stained by adding DAPI (1 μg/mL) and Triton X-100 (0.1%). Images were acquired on an Amnis ImageStreamX imaging flow cytometer (Merck Millipore) with the 60X objective. Data were analyzed using IDEAS 6.2 software following a method adapted from Pelletier et al. (25 (link)). Monocyte subpopulations were gated among in-focus single cell events, using the same gating strategy as for flow cytometry analysis. Average measurements from multiple masks selected after visual inspection were used to accurately represent the cell surface (bright field area in Ch01, 3 masks) and nuclei (DNA dye intensity in Ch07, 4 masks). These average cellular and nuclear areas were used to create a combined feature to calculate the “per cell” average cytoplasmic area (area of the cell reduced by the area of the nucleus) and N/C ratio (average nuclear area divided by the average cytoplasmic area).
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3

Granulocyte Eosinophil Activation Assay

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Granulocytes (80 µl) and assay buffer (10 µl) were incubated in a water bath (5 min, 37 °C). Metabolite solutions (10 µl, final concentration (conc.) 0.01 nM, 0.1 nM, 0.5 nM, 1 nM, 5 nM, 10 nM, 100 nM, 1 µM, 1% DMSO in assay buffer) were added (5 min, 37 °C). The incubation was stopped with 250 µl of 0.25% BD Cell-Fix™ Solution (1:10 with sterile water followed by 1:4 with assay buffer, BD Biosciences, Heidelberg, Germany) and immediate placement on ice (≥ 5 min). Flow cytometric analysis was performed with a Navios 3/10 (Beckman Coulter). Granulocytes were determined by FSC and SSC properties. Eosinophils were discriminated from neutrophils by autofluorescence properties at 560 nm (FL2). 1000 eosinophils were acquired. Eosinophil shape change was calculated as percentage increase of the mean FSC units.
For DP2 inhibition experiments, granulocytes (80 µl) and fevipiprant (10 µl, final conc. 0.01 nM, 0.05 nM, 0.1 nM, 1 nM, 5 nM, 10 nM, 100 nM, 500 nM, 1 µM, 10 µM) were incubated in a water bath (5 min, 37 °C). Metabolite solution (10 µl, EC70 concentration) was added for 5 min (37 °C). The reaction was stopped and cells were analyzed as described above.
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4

NF-κB Activation in Monocytic Cells

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U937 monocytic cells containing a 5x NF-κB green fluorescence protein reporter cassette [19 (link)] were cultivated in RPMI 1640 containing 7.5% fetal bovine serum. The cells were pretreated for 1 ½ hours with reconstituted HDL (1-50 µg/mL), lipoprotein deficient serum or 7% apoB-depleted serum. Subsequently, the cells were stimulated for 24 hours with lipopolysaccharide (LPS) (50 ng/mL) (Sigma, Darmstadt, Germany), collected by centrifugation at 400 g for 7 minutes and fixed with 100 μL BD CellFIX solution (BD Biosciences, Franklin Lakes, NJ, USA). The expression of NF-κB was assessed by flow cytometry and cytokines were quantified using a multiplex bead-based immunoassay (eBioscience, San Diego, CA, USA).
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5

Multicolor Flow Cytometry Analysis

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Cells were resuspended in fluorescence-activated cell sorting (FACS) buffer (5% fetal calf serum plus 5 mM EDTA in PBS) and incubated with conjugated monoclonal antibodies (mAb). The mAb used, phycoerythrin (PE)-conjugated anti–Ly-6G (clone RB6-8C5, 125931, 1/400), fluorescein isothiocyanate (FITC)-conjugated anti-CD11b (clone M1/70, 11011241, and 1/200), and allophycocyanin (APC)-conjugated anti-F4/80 (clone BM8, 17480182, 1/800), eF450-conjugated anti-CD4 (clone RM4-5, 48004282, 1/200), PE-conjugated anti–Foxp3 (clone FJK‐16 s, 12577382, 1/100), FITC-conjugated anti-CD25 (clone PC61.5, 53025382, 1/400), APC-conjugated anti-Arginase-1 (clone A1exF5, 17369782, 1/100), APC-conjugated anti-EGR2 (clone erongr2, 17669182, 1/100), were all from eBioscience. PE-conjugated anti-CD206 (clone CD68C2, 141705, 1/100) and PE-conjugated anti-IL-6 (clone MP5-20F3, 504504, 1/100) were from Biolegend. Cells (1 × 106) were incubated with appropriate conjugated antibodies for 30 min at 4 °C in the dark. Stained cells were subsequently washed twice with FACS buffer and fixed in BD CellFIX solution (BD Biosciences). Flow cytometric analyses were performed on LSRII cytometer (Becton Dickinson) using FACS Diva6 (Becton Dickinson) and FlowJoX (Tree Star) software for data processing.
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6

Multicolor Flow Cytometry of Cervicovaginal Cells

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Neutrophil populations were analyzed in whole blood and cervicovaginal cells. Cervicovaginal cells were filtered using a 35 µm filter (Corning Falcon; USA). Then, cervicovaginal cells and whole blood were incubated with the antibodies listed in Table 2, washed, and fixed with FACS lysing buffer (BD, Biosciences) or BD cell Fix solution (BD, Biosciences). A 14-color panel containing neutrophil maturation and activation surface markers was used. Phenotyping was performed on a Fortessa instrument (BD, Biosciences) using DIVA (BD) and FlowJo (Tristar, USA) software. The gating strategy for cervicovaginal cytobrushes is described in Supplementary Figure 1.
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7

Immunophenotyping of T Cell Subsets

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Fourfold whole blood staining with directly conjugated antibodies for CD4 (Pacific Blue, clone RPA-T4), CD45RA (FITC, clone HI100), CD25 (APC, clone M-A251), CD39 (RPE, clone TU66), CD73 (RPE, clone AD2), and CD26 (RPE, clone M-A261) (all purchased from BD Biosciences, Heidelberg, Germany), was performed on 100 μl of each sample (due to technical reasons, 2 patients could not be analysed by FACS; AAV: n = 29, HC: n = 12). Optimal antibody concentrations were determined by serial dilution. After antibody incubation, red blood cells were lysed using BD FACS lysing solution (BD Biosciences, Heidelberg, Germany) followed by thorough washing with phosphate buffered saline (PBS, Sigma Aldrich) containing 2 mM EDTA (Sigma Aldrich) and 3% (w/v) bovine serum albumine (Serva Electrophoresis GmbH, Heidelberg, Germany) and finally fixation with BD cellFIX solution (BD Biosciences, Heidelberg, Germany). For compensation BD compBeads (BD Biosciences, Heidelberg, Germany) were stained in a similar manner as described above. Flow cytometry was performed on a BD FACS Canto II cytometer using negative and fluorescence-minus-one controls and data analysis was performed using FlowJo software version 5.2 (FlowJo LLC, Ashland, USA).
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8

NF-κB Activation in Monocytic Cells

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U937 monocytic cells containing a 5x NF-κB- green fluorescence protein reporter cassette were cultivated in RPMI 1640 containing 7.5% fetal bovine serum in 1.1 mL micro tubes (Bioquote, York, UK) (50.000 cells/tube). The cells were pretreated for 1 ½ hours with 2.5% full serum, 5% apoB-depleted serum, 10% LPDS or rHDL (50 μg/ml). Subsequently, the cells were stimulated for 24 hours with lipopolysaccharide (LPS) (50 ng/ml) (Sigma, Darmstadt, Germany), collected by centrifugation at 400 × g for 7 minutes and fixed with 100 μL BD CellFIX solution (BD Biosciences, Franklin Lakes, NJ, USA). The expression of NF-κB was assessed by flow cytometry. The supernatants were collected and used for cytokine quantification by flow cytometry using a multiplex bead-based immunoassay (eBioscience, San Diego, CA, USA).
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9

Quantifying Transfection Efficiency via Flow Cytometry

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Using trypsin/EDTA (0.04%/0.03%), cells were detached, washed, and fixed in 1× CellFix solution (BD Biosciences, Heidelberg, Germany). A total of 10,000 cells was analyzed by FACScan flow cytometer (Becton Dickinson, Heidelberg, Germany). Cells expressing eGFP were detected using the FL1 (green) channel and measuring the fluorescence at 509 nm. FACS data were displayed in histograms. For the evaluation, a marker M1 was set, which contained maximum of approximately 1.5% of control cells (cells treated with transfection medium without mRNA). Using histogram statistics of the CellQuest Pro Software (Becton Dickinson), the percentage of eGFP positive cells was determined to assess the transfection efficiency. Geo Mean (geometric mean) values show the strength of the fluorescence intensity. Higher Geo Mean values reflect stronger fluorescent intensity, indicating a higher production of eGFP.
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10

Monocyte Uptake of Labeled Dendrimers

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CD14+ cells (105 cells per well in 1 mL RPMI-1640 medium containing 10% FBS) were seeded in 12-well plates (TPP, Trasadingen, Switzerland). After 24 h, the medium was replaced with either RPMI-1640 medium containing 10% FBS or cell culture RPMI-1640 medium containing 3 mg/mL bovine serum albumin (BSA) or RPMI-1640 medium without any proteins. Rhodamine B-labeled dPG NPs were diluted in the respective cell culture medium (final concentration dPGOH-RB 50 μg/mL and dPGS-RB 20 μg/mL) and pre-incubated for 1 h (at 37°C) such that a protein corona can form. Cell culture medium from the monocytes was then replaced with the respective cell culture medium containing the NPs and incubated for 1 or 6 h, respectively. Later, the cells were rinsed with PBS and detached using trypsin (PAN Biotech GmbH), washed again using PBS and fixed using 100 μL 1× CellFix solution (BD Biosciences). Uptake was analyzed using an FACS Aria III (BD Biosciences), equipped with a blue laser (488 nm) and fluorescence detector (585/42 nm) using a 70 μm nozzle.
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