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69 protocols using pharm lyse lysing buffer

1

Evaluating Cervical Cell Aneuploidy

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The cervical cells were subjected to cellular lyses using Pharm Lyse lysing buffer (Becton Dickinson, New Jersey, USA) for 30 minutes. After a quick wash, the cells were incubated in 0.5 mL RNA solution (100 µg/mL) supplemented with propidium iodide, a fluorescent reagent that intercalates DNA bases. The DNA fluorescence was measured using flow cytometry, through laser excitation at 488 nm and reading above 600 nm; and DNA index was determined by comparison with labeled normal diploid cells using the ModFitLT V3.0 software (Verity Software House Inc., Topsham, USA). The presence of two peaks on a histogram with an index greater than 1.16 (hyperploidy) or less than 1.00 (hypoploidy), each with more than 10% of the cell population analyzed in the area corresponding to G0–G1 of the cell cycle, was considered to be aneuploidy [15] (link).
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2

Aneuploidy Detection in Cervical Cells

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Cervical cells were lysed using Pharm Lyse lysing buffer (Becton Dickinson, New Jersey, USA) for 30 minutes prior incubation with RNA solution (100 μg/mL) and propidium iodide. DNA fluorescence was measured by flow cytometry (laser excitation at 488 nm and emission above 600 nm), and DNA index was estimated through by comparison the ratio of the DNA content of cells analyzed with labeled blood diploid cells using the ModFitLT V3.0 software (Verity Software House Inc., Topsham, USA). The presence of two peaks on a histogram with a DNA index greater than 1.16 (hyperploidy) or less than 1.00 (hypoploidy), each with more than 10% of the cell population analyzed in the area corresponding to G0–G1 of the cell cycle in the sample, was considered to be aneuploidy [28 (link)].
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3

Immunophenotyping of Murine Leukocytes

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After treatment, all mice were weighed, blood were collected by cardiocentesis under general anesthesia using a disposable syringe with needle (20-gauge), and liver and spleens were dissected and weighed (23 (link)). Collected blood (1 ml/mouse) was lysed with 1X Pharm Lyse™ lysing buffer (BD Biosciences) to destroy red blood cells and leukocytes, as described previously (21 (link)). Following centrifugation at 1,500 × g for 15 min at 4°C, white blood cells were collected and stained with phycoerythrin (PE)-labeled anti-mouse CD3 (BD553062; BD Biosciences, San Jose, CA, USA), PE-labeled anti-mouse CD19 (BD553786; BD Biosciences), fluorescein isothiocyanate (FITC)-labeled anti-mouse CD11b (BD553310; BD Biosciences) and FITC-labeled anti-mouse Mac-3 (BD553324; BD Biosciences) antibodies at 1:12 dilution of each for 30 min at 4°C. All samples were analyzed by flow cytometry (BD Biosciences) and quantified using CellQuest software version 5.2.1 (BD Biosciences), as previously described (21 (link)).
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4

Evaluation of Immune Cell Populations in Mouse Blood and Spleen

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The blood and spleen of each mouse was collected. Splenocytes were isolated from the spleen in order to evaluate NK cell activity, as previously described (25 (link),26 (link)). To analyze blood samples (0.2 ml each) for cell markers, red blood cells were lysed using 1X Pharm Lyse lysing buffer (BD Pharmingen, San Diego, CA, USA), according to the manufacturer's instructions. After centrifugation at 1,500 × g for 15 min at 4°C, white blood cells were collected and stained with phycoerythrin (PE)-labeled anti-mouse CD3 (BD553062, BD Biosciences, San Jose, CA, USA), PE-labeled anti-mouse CD19 (BD553786, BD Biosciences), fluroscein isothiocyanate (FITC)-labeled anti-mouse CD11b (BD553310, BD Biosciences) and FITC-labeled anti-mouse Mac-3 (BD553324, BD Biosciences) antibodies (the dilution of each antibody was 1:12) for 30 min at 4°C. The cells were washed with PBS and analyzed for cell marker population by flow cytometry, as previously described (25 (link),26 (link)).
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5

Identification of Monocyte Subsets

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Monocyte subpopulations were identified with flow cytometry using the lysis-no-wash strategy (BD Pharm Lyse lysing buffer, Becton Dickinson) on fresh EDTA blood. A total of 100 μl of EDTA blood was stained by monoclonal antibodies (CD16 FITC NKP15 Becton Dickinson, CD14 PE RMO52 Beckman Coulter, HLA-DR Immu357 PC5.5 Beckman Coulter, and CD45 PC7 J33 Beckman Coulter). Surface expression was assessed using FC500 and CytoFLEX flow cytometer (Beckman Coulter) and analyzed with Kaluza software version 2.1 (Beckman Coulter). The applied gating strategy was in short; monocytes were selected in the SSC/CD45+ plot, gated to SSC/HLA-DR + plot, identifying monocytes as CD45+ HLA-DR + cells with monocyte scatter properties. Exclusion of lymphocytes, and natural killer cells was performed by excluding CD45+ HLA-DR+ CD14– CD16– cells. In the CD14/CD16 plot, the percentages of gated monocyte subsets (classical CD14++CD16−), intermediate (CD14++CD16+), and nonclassical monocytes (CD14+CD16++) were used for analyses. Identification of monocytes subsets follows current recommendations (21 (link)).
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6

Characterizing Monocyte Subsets and Platelet Complexes

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Monocyte subpopulations, platelet complexes and expression markers were identified with flow cytometry. Using the lysis‐no‐wash strategy (BD Pharm Lyse lysing buffer, Becton Dickinson, Franklin Lakes, NJ, USA), 50 μL EDTA blood was stained by monoclonal antibodies (CD45 Chrome Orange clone J33 Beckman Coulter, HLA‐DR PE clone immu‐357 Beckman Coulter, CD14 PC7 clone 61D3 Bioscience, CD16 FITC clone CB16 eBioscience, CD3 APC‐750 clone UCTH1 Beckman Coulter, CD56 APC clone N901 Beckman Coulter, CD192 BV421 clone 48607 Becton&Dickinson, CD11b BV785 clone ICRF44 Biolegend, CD41 PC5.5 clone Hip8 Biolegend) and measured with CytoFLEX flow cytometer (Beckman Coulter, Brea, CA, USA). The gating strategy applied is shown in Figure S1, gates were set with the fluorescence minus one method.24, 25 Data were analyzed with Kaluza 3.1 software (Beckman Coulter). Characterization of monocytes subsets is according to current recommendations.24, 25
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7

Characterization of Monocyte Subsets by Flow Cytometry

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Monocyte subpopulations, consisting of CD14++CD16 classical monocytes, CD14++CD16+ intermediate monocytes, and CD14+CD16+ non-classical monocytes, were identified with the FC500 flow cytometry (Beckman Coulter, Brea, USA) using the lysis-no-wash strategy (BD Pharm Lyse lysing buffer, Becton Dickinson) with 100 μl fresh EDTA blood. Cells were stained by monoclonal antibodies (CD16 FITC Leu11a, Becton&Dickinson; CD14 ECD RM052, Beckman-Coulter; CD45 PC5 J.33, Beckman-Coulter) and subsequently analyzed with Kaluza software version 1.5a (Beckman Coulter).
The full gating strategy is displayed in Supplementary Figure 1. In short, monocytes were gated in SSC/CD45+ plot, identifying monocytes as CD45+ cells with monocyte scatter properties. Exclusion of lymphocytes and natural killer cells was performed by excluding CD14/CD16 negative cells. Percentages of monocyte subsets (CD14++CD16, CD14++CD16+, and CD14+CD16+) were identified in the CD14/CD16 plot. For determination of the gates setting, the fluorescence minus one method was applied. Identification of monocyte subsets follows current international recommendations (20 (link), 21 (link)).
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8

Liver and Spleen Lymphocyte Isolation

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BALB/c mice were sacrificed via neck dislocation after anesthesia. Liver perfusion in the mice was performed using 1 × Dulbecco’s phosphate-buffered saline (DPBS) (without Ca2+ and Mg2+) via the portal vein. Harvested livers were washed with PBS. The tissue was quickly minced with scissors and placed in 50-ml conical tubes. Tissues were dissociated into single cell suspensions using an Ultra Turrax® Tube Disperser (IKA, Königswinter, Germany). Lymphocytes were separated using a 40% Percoll solution and gradient centrifugation. The supernatant and lipid layer were discarded, and the cells were washed twice with DPBS. Red blood cells were lysed using BD Pharm Lyse™ Lysing Buffer (Becton Dickinson and Company, Franklin Lakes, NJ, USA), leaving nonparenchymal cells. The spleen was removed and ground into a cell suspension, which was filtered into a single-cell suspension using a 70-μm cell sieve (Becton Dickinson). Red blood cells were lysed, and the remaining cells were washed twice with 1× DPBS to obtain splenic lymphocytes.
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9

Isolation and Analysis of Mouse Splenocytes

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Upon termination of the treatment, all mice were individually weighed and blood samples, as well as the liver and spleen of the mice were individually collected. The collected spleens were used for the isolation of splenocytes and measurement of natural killer (NK) cell activity, as previously described (15 (link)). A blood sample of 1 ml from each mouse was lysed to destroy the red blood cells using 1X BD Pharm Lyse™ lysing buffer (BD Biosciences, Franklin Lakes, NJ, USA) according to the manufacturer's protocol, and leukocytes were collected as previously described (15 (link)). Phycoerythrin (PE)-labeled anti-mouse CD3, PE-labeled anti-mouse CD19, fluorescein isothiocyanate (FITC)-labeled anti-mouse CD11b and FITC-labeled anti-mouse Mac-3 antibodies (all dilution 1:40) were used to stain the isolated leukocytes for 30 min, and then all samples were washed with phosphate-buffered saline (PBS). After this, all samples were analyzed using flow cytometry (BD FACSCalibur; BD Biosciences) to measure the percentages of white blood cell markers, as previously described (15 (link)).
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10

Flow Cytometry Immunophenotyping Protocol

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Antibody reagent cocktails were made in 5 ml round-bottom tubes, immediately prior to use, as specified in Table 1. One hundred microliters of cells separated (approximately 1 × 106 cells) in phosphate-buffered saline (PBS) were added. Tubes were incubated for 20 minutes in the dark at room temperature. Red blood cells (RBCs) were lysed by adding 1 ml of 1X BD Pharm Lyse lysing buffer to each tube followed by 10 minutes of incubation in the dark at room temperature. Acquisition and analysis were done using a FACSCanto flow cytometry (Becton Dickinson Biosciences, San Jose, California USA). One hundred thousand events were analyzed, and an isotype-matched negative control was used with each sample [12 (link)].
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