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12 protocols using attune software

1

iPSC-derived Endothelial Cell Isolation

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iPSCs derived ECs were dissociated by incubation with 0.05% Trypsin-EDTA (Thermo Fisher Scientific 25300054) for 5 min at 37 °C. A total of 1 × 106 single cells were resuspended in 100 μl FACS buffer (PBS supplemented with 10% FBS) and stained by incubation with 5 μl CD144-APC antibody for 30 min at 4 °C in the dark. The cells were washed twice with PBS before resuspension in 1 ml PBS for FACS experiment on an Attune NxT Flow Cytometer and data were analyzed with Attune software (Thermo Fisher Scientific).
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2

Annexin V-FITC Apoptosis Assay

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Approximately 2 × 105 cells (A375) were seeded in cell culture flasks (25 cm2), and the cells were allowed to grow up for 24 h. After removing of the used medium, the substance loaded fresh medium was reloaded (or a blank fresh medium as a control). After 24 h and 48 h, the cells were harvested, centrifuged (1200 rpm, 4 °C), and washed twice with PBS (w/Ca2+ and Mg2+, 1 mL). The cells were counted and approximately 1∙106 cells were washed with Annexin V binding buffer (BioLegend®, San Diego, USA) and treated with propidium iodide solution (3 µL, 1 mg/mL) and Annexin V-FITC (5 µL, BioLegend®, San Diego, CA, USA) for 15 min in the dark at room temperature. After adding Annexin V binding buffer (400 µL) the suspension was analyzed using Attune® FACS machine. After gating for living cells, the data from detectors BL-1A and BL-3A were collected (20,000 events) in technical triplicates. The assay was performed in duplicates; cell distribution was calculated using Attune® Software (ThermoFisher Scientific, Braunschweig, Germany).
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3

Evaluating Combination Therapies on Myeloma Cells

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Myeloma cell lines (5×104 per well) were incubated with CPI203 (kindly provided by Constellation Pharmaceuticals, Cambridge, MA, USA) and/or lenalidomide (Selleck Chemicals LLC, Houston, TX, USA) plus dexamethasone (Merck, S.L., Darmstadt, Germany) at indicated doses in triplicates. MTT [3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide] assay (Sigma-Aldrich, St Louis, MO, USA) was used to evaluate the effect of the drugs on cell proliferation.
Primary cells were labeled with CellTracker™ Red CMPTX dye (Thermo Fisher) following the manufacturer’s protocol and co-cultured with the mesenchymal stromal cell line stromaNKtert in the presence of 10 ng/mL IL-6 (RnD Systems, Minneapolis, MN, USA). Cell proliferation was analyzed in an Attune acoustic focusing cytometer using Attune software (Thermo Fisher).
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4

Purification and Characterization of CD34+ Cells

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Unmanipulated UCB, BM or mobilized PB CD34+ cells or cells from cultures treated with cytokines alone or cultures treated with VPA were stained with anti-human CD34-APC (BD Pharmingen), CD90-FITC (Thermo Fisher Scientific), CD201-PE (Bio-Legend), CD45RAef-506 (Thermo Fisher Scientific), CD38 SB-702 (Thermo Fisher Scientific) for 30 min at 4°C, washed and analyzed using an Attune flow cytometer (Thermo Fisher Scientific). Analyses were performed with Attune software (Thermo Fisher Scientific) and FlowJo Software (BD Biosciences). Compensation parameters are assessed by using AbCTM Total Antibody Compensation Bead Kit (Thermo Fisher Scientific) according to the manufacturer instructions. Doublet exclusion was performed by FSC-H/FSC-A selection followed by SSC-H/SSC-A selection. Gating of positive/negative population was performed by using fluorescence minus one control (FMO) strategy (Papa et al., 2020b (link)). Purification of the various CD34+ cell subpopulations is performed in media supplemented with cytokines or cytokines and VPA using a BD FACSAria (BD Bioscience).
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5

Characterization of Anti-PD-L1 and Anti-CD19 scFv T Cells

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For detecting the anti-PD-L1 scFv, a PD-L1-Fc Fusion protein was used (Sino Biological). For detecting the anti-CD19 scFv, a monoclonal anti-FMC63 antibody was used (Acro Biosystems). For T cell phenotype characterization, the following antibodies were used: mouse anti-human CD3 (clone: UCHT1), TCRαβ (clone: IP26), CD4 (clone: RPA-T4), CD8 (clone: RPA-T8), CD45RA (clone: HI100), CD62L (clone: DREG-56), CCR7 (clone: G043H7) from BioLegend. To evaluate cytotoxicity, Live/Dead Fixable Yellow (Thermo Fisher Scientific) and Annexin V (BioLegend) were used to stain the effector and tumor cells in the co-culture. To examine the degranulation, CD107a (BioLegend) and Granzyme B (BD) were used in the assay. FACS data were acquired on Attune (Thermo Fisher Scientific) and analyzed with Attune software.
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6

Multicolor Flow Cytometry for Stem Cell Enumeration

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For each blood draw, triplicate samples of 100 µL of heparinized whole blood was stained using the following four-color immunostaining panel: CD31-FITC, CD34-PerCP, CD45-PO, and CD133-PE. For eight of the study participants, a fifth color was added: CD90-v421. Staining was performed as recommended by Thermo Fisher Scientific (Waltham, MA, USA) for whole blood staining followed by a “no-wash” procedure involving Cal-Lyse® fixation of white blood cells and lysing of red blood cells. In brief, samples were stained in the dark at room temperature for 15 minutes followed by the addition of 100 µL of Cal-Lyse® Lysing solution and fixation for 10 minutes at room temperature. Red blood cells were then lysed by the addition of 1 mL of deionized water and further 10 minutes incubation in the dark at room temperature. Samples were stored at 4°C in the dark and acquired by flow cytometry within 24 hours using an acoustic-focusing Attune™ flow cytometer (Thermo Fisher Scientific). Files of 300,000–600,000 events were collected for each triplicate sample. Data on stem cell numbers were analyzed by the Attune software (Thermo Fisher Scientific) that provides results as cell per microliter of sample and compensated for the dilution factor that was part of the immunostaining protocol, so the results were converted to stem cell numbers per microliter of whole blood.
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7

Flow Cytometry Measurements with Attune Acoustic

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Flow cytometry measurements were performed with an Attune™ Acoustic Flow Cytometer (Life Technologies) with 488 nm excitation. Forward-scatter characteristics (FSC) and side-scatter characteristics (SSC) were detected as small-angle and large-angle scatters of the 488 nm laser, respectively. SYFP2 fluorescence was detected using a 530/30 nm (channel BL1) band-pass filter set. Data were analyzed using the Attune™ software (Life Technologies). A total of 100,000 events was recorded per sample, and electronic gating was applied on the densest subset of cells on the basis of forward- vs. side-scatter height. The same gate was used to estimate geometric mean levels of SYFP2 fluorescence.
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8

Monocyte-Platelet Aggregation Assay

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Monocyte activation and formation of platelet–monocyte aggregates were assessed under static and flow conditions. Therefore, suspensions of PBMCs and platelets were prepared as described above and directly incubated with the 5 mm Ø control and polymer surfaces for 5 min. Subsequently, the cell suspension was collected and stained with monoclonal antibodies obtained from eBioscience (San Diego, CA, USA) for anti-human CD14-FITC, CD62P-PE and anti-human CD11b-PE-Cy7. Flow cytometry measurements were performed with an Attune® Cytometer (Life Technologies GmbH, Darmstadt, Germany) and analyzed using Attune® Software (Life Technologies GmbH, Darmstadt, Germany).
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9

Comprehensive Immune Cell Profiling

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Cells were analyzed by flow cytometry with Attune Nxt (Thermofisher) and FlowJo software (Tree Star). The following monoclonal antibodies were used: anti-CD34 (RAM34), anti-CD48 (HM48-1), anti-CD117 (2B8), anti-Flt3 (A2F10.1), anti-Sca-1 (D7), anti-B220 (RA3-6B2), anti-CD19 (1D3), anti-CD3 (145-2C11), anti-CD4 (GK1.5), anti-CD8 (53-6.7), anti-CD11b (M1/70), anti-Gr-1 (RB6-8C5), anti-Ter119 (TER119), anti-CD11c (N418), anti-CD8(53-6.7), anti-PDCA1 (129C1), anti-CD24 (M1/69), anti-SIRPa (P84), anti-CD103 (2E7), anti-CD45 (S18009F), anti-CD207 (4C7), anti-CD115 (AFS98), anti-LY6C (HK1.4), anti-SiglecH (551), anti-CLEC9A (7H11), anti-CD80 (16-10A1), anti-CD86 (GL-1), anti-CD40 (3/23), anti-H2Kb (AF6-88.5), anti-IA/IE (M5/114.15.2) and anti-BrdU (3D4) from Biolegend. Cells incubated with biotinylated monoclonal antibodies were incubated with fluorochrome-conjugated streptavidin–peridinin chlorophyll protein–cyanine 5.5 (551419; BD), streptavidin–allophycocyanin-Cy7 (554063; BD), streptavidin-super bright 650 (Biolegend). In all the FACS plots, indicated are the percentages (%) of the gated fraction. Data were acquired on a Attune Nxt Acoustic focusing cytometer using Attune software (life technologies) and analyzed using FlowJo (Treestar Inc).
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10

Immunophenotyping by Flow Cytometry

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Cells were incubated with primary and secondary antibodies for 30 minutes at 4 °C. The stained cells were analyzed on an Attune acoustic focusing cytometer (Applied Biosystems, Carlsbad, CA). Data were analyzed with Attune software (Applied Biosystems) or FlowJo software (BD Biosciences, San Jose, CA).
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