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45 protocols using anti cd45 apc cy7

1

Comprehensive Immune Cell Profiling

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After washing with saline solution, single cell suspensions were stained for 20 min at 4 °C, with two separate staining mixtures: (a) anti-CD45-APC-Cy7 (#103116 BioLegend® (San Diego, CA, USA), Clone 30-F11), anti-CD3ε-PerCP-Cy5.5 (#100217 BioLegend®, Clone 17A2), anti-CD4-PE (#553048 BD Biosciences® (Franklin Lakes, NJ, USA), Clone RM4-5), anti-CD8a-APC (#100711BioLegend®, Clone 53-6.7) or (b) anti-CD45-APC-Cy7 (#103116 BioLegend®, Clone 30-F11), anti-CD11c-APC (#117309BioLegend, clone N418), anti-CD11b-PE (#101207BioLegend®, Clone M1/70), anti-LyG-FITC (#127605BioLegend®, Clone 1A8) and anti-NK1.1-Brilliant Violet 605 (#108739, BioLegend®, Clone PK136). After washing in FACS buffer (saline solution with 1% fetal bovine serum), cells were fixed in 4% paraformaldehyde for 30 min at room temperature before taking samples out of the BSL3 area. Cells were again washed, resuspended in FACS buffer and acquired using FACS Symphony A5 with BD FACS Diva software. Cell populations were gated and quantified by FlowJo10.7 software. Gating strategies used for analysis are presented in Figure S1.
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2

Isolation and Characterization of Synovial Fibroblasts

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Isolation of SFs was performed from both hind paws. The ankle joints were dissected, and the tissues were disaggregated by incubation for 30 min at 37 °C in an enzymatic digestion medium consisting of DMEM, 10%heat-inactivated FBS, collagenase (0.5 mg ml−1) from Clostridium histolyticum (Sigma, C5138) and 0.03 mg ml−1 DNase (Sigma, 9003-98-9). Upon washing the cells with PBS containing DNase, they were blocked in 1% BSA in PBS and Fc blocker (unlabelled anti-CD16/32, Biolegend 101302) for 10 min at 4 °C and stained with fluorophore-conjugated antibodies for 20 min at 4 °C (anti-Pdpn PE-Cy7, Biolegend 127411; anti-Thy1 A647, Biolegend 105318; anti-CD31 APC/Fire 750, Biolegend 102433; anti-CD45 APC-Cy7, Biolegend 103116; anti-Ter119 APC-A780, eBioscience 47-5921-80). After washing with PBS, cells were resuspended in FACS buffer (PBS, 1%BSA). Sorting of cells was performed with BD FACSAria III and the BD FACSDiva software, and dead cells were excluded by DAPI staining. Sorting gaiting for single-cell RNA-seq/ATAC-seq and bulk RNA-seq was different (Additional file 1: Fig. S1B). For sorted populations, purity and viability were determined by reanalysis for the target population based on cell surface markers immediately post-sorting. Purity was > 99% for each target population.
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3

Assessing NK Cell Activation in Cancer

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NCI-H1960, A549 and NCI-H1975 cells were seeded in 6-well plates, incubated overnight and treated with docetaxel and cisplatin (concentrations as described above). After 24 hours of treatment, the appropriate conditions were treated with human aCD70 or isotype control and co-cultured with NK cells at a 5:1 ratio. After washing, cells were stained with the following antibodies: anti-CD45 APC-Cy7 (1:50, Clone 2D1, Biolegend), anti-CD3 PE-Cy7 (1:100, Clone SK7, Biolegend), anti-CD56 PE-CF594 (1:25, Clone NCAM16.2, BD Biosciences), anti-CD69 PerCP-Cy5.5 (1:100, Clone FN50, Biolegend) and Live/Dead Fixable Aqua (1:50, Invitrogen) for 30 minutes at 4°C. Acquisition was performed on the Novocyte Quanteon (Agilent technologies).
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4

Neutrophil Depletion in MmuPV1 Infection

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For neutrophil depletion experiment, 250 μg of anti-Ly6G (BioXCell, clone 1A8) or 250 μg of isotype control (BioXCell, rat IgG2a) was delivered by intraperitoneal injection three times per week, starting at 7 wk post-MmuPV1 infection until 11 wk postinfection. To assess neutrophil depletion, anti-Gr1 PE-Cy5 (BioLegend, clone RB6-8C5), anti-CD11b BV605 (BioLegend, clone M1/70), and anti-CD45 APC-Cy7 (BioLegend, clone 30-F11) were used for flow cytometry.
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5

Tumor Tissue Dissociation Protocol

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Weighed tumors were minced and allowed to digest in a mixture of 1mg/ml of collagenase P (Roche 11213857001), 0.1 mg/ml Collagenase I (Sigma, C0130), 0.1 mg/ml Dispase II (Roche, 04942078001) and DNase (5MU/ml, Calbiochem, 260913) in DMEM media at 37°C for 30 min. The tissue lysate was filtered through a 40 µm mesh prior to immunostaining. The resulting single-cell suspension was stained with fixable viability dye eFluor 780, anti-CD45-APC-Cy7 (103115, 1:200), anti-CD11b-FITC (101205, 1:100) and anti-Ly6/C-PE (128007, 1:100) (all from BioLegend). The percentage of positive cells were analyzed by FlowJo and gated on CD45 positivity. Unstained, live/dead only, and single stain served as control. Doublets were gated out using forward-scatter width/height and side-scatter width/height event characteristics.
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6

Sputum Immune Cell Profiling by Flow Cytometry

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Sputum cells were blocked with anti-CD16/CD32 antibodies (BioLegend, USA) for 10 min and then stained with Live_Dead (Zomnie Aqua, BioLegend) for 20 min at 4 °C. Human induced sputum cells were then stained with the following antibodies: anti-CD45 (APC/Cy7; BioLegend), anti-CD11c (APC; BioLegend), anti-CD68 (PE; Invitrogen, CN), anti-CD86 (PE/Dazzle594; BioLegend), anti-CD16 (Percp/Cy5.5; BioLegend), anti-CD11b (PE/Cy7; BioLegend), and anti-CD15 (FITC; BioLegend). Flow cytometry was performed with a Cytek Dxp Athena flow cytometer, and the data were analyzed by using FlowJo (version 10) software.
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7

Tumor Tissue Dissociation Protocol

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Weighed tumors were minced and allowed to digest in a mixture of 1mg/ml of collagenase P (Roche 11213857001), 0.1 mg/ml Collagenase I (Sigma, C0130), 0.1 mg/ml Dispase II (Roche, 04942078001) and DNase (5MU/ml, Calbiochem, 260913) in DMEM media at 37°C for 30 min. The tissue lysate was filtered through a 40 µm mesh prior to immunostaining. The resulting single-cell suspension was stained with fixable viability dye eFluor 780, anti-CD45-APC-Cy7 (103115, 1:200), anti-CD11b-FITC (101205, 1:100) and anti-Ly6/C-PE (128007, 1:100) (all from BioLegend). The percentage of positive cells were analyzed by FlowJo and gated on CD45 positivity. Unstained, live/dead only, and single stain served as control. Doublets were gated out using forward-scatter width/height and side-scatter width/height event characteristics.
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8

Tumor Immune Cell Profiling

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Tumors were harvested, weighed, minced, and digested for 45 minutes, with gentle shaking, at 37°C in HBSS containing 7mg/ml collagenase D and 200 μg/ml DNase-I (Roche). Single-cell suspensions were stained with antibodies including anti-CD45-APC-Cy7, anti-CD3-Vioblue, anti-CD8-PCP, anti-CD4-FITC, anti-Foxp3-PE, anti-CD11b-APC, anti-GR-1-PE-Cy7, Anti-GATA3-PE, anti-T-bet-PE-Cy7, anti-RORγt-APC (BioLegend or eBioscience); and anti-Annexin-V-Alexa647 (BD Pharmingen). Cells were fixed/permeabilized using reagents from the Foxp3 staining kit (eBioscience). Flow cytometry was performed on a Miltenyl MACS Quant10 Analyzer. Total cells were enumerated using the flow cytometer.
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9

Multi-Lineage Tumor Cell Isolation

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Briefly, the fresh tissue samples from two human PC tissues and seven mouse-derived allografts of KPC1199 cells were mechanically chopped and digested by collagenase IV at 37 °C for 30 min. The digested suspension was combined with DNase at room temperature for 5 min, washed twice with phosphate-buffered saline buffer containing 2% serum, and then filtered through the 100 μm filter. We used markers of CD29, PDPN, EpCAM, and CD45 to separate tumor epithelial cells (CD45CD29 or PDPNEpCAM+), CAFs (EpCAMCD45CD29 or PDPN+), and tissue leukocytes (CD29 or PDPNEpCAMCD45+) in human and mouse tumor specimens, respectively. The digested single cells were washed twice and centrifuged for 5 min at 500× g, and then 1 μg/mL of antibody was added. Then, the samples were kept at 4 °C for 30 min in a dark place. Flow cytometry was employed using a BD Flow Cytometry Analysis Celesta cell sorter (Becton Dickinson, New York, NY, USA). The side-scatter width versus side-scatter region and the forward-scatter width versus forward-scatter height were applied to remove dead cells and cell clumps. Antibodies including anti-EpCAM-PerCR/Cy5.5 (BioLegend, San Diego, CA, USA, #324214), anti-CD45-APC-Cy7 (BioLegend, #368515), and anti-CD29-Alexa Fluor® 488 (BioLegend, # 303015) were verified according to the manufacturer’s website.
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10

Tumor Immune Cell Profiling

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Tumors were harvested, weighed, minced, and digested for 45 minutes with gentle shaking at 37°C, in HBSS containing 7 mg/ml Collagenase D and 2 mg/ml DNase-I (Roche). Single cell suspensions were stained with antibodies including anti-CD45-APC-Cy7, anti-CD3-Vioblue, anti-CD8-PCP, anti-CD4-PCP, anti-Foxp3-FITC, anti-CD11b-APC, CD11b-PCP, anti-Gr-1-PE-Cy7, anti-Ly6C-PE, and anti-Ly6G-PE-Cy7 (BioLegend or eBioscience); anti-CCR2-APC or control Rat IgG2B-APC antibody were obtained from R&D. Cells were fixed/permeabilized using reagents from the Foxp3 staining kit (eBioscience). Flow cytometry was performed on a Miltenyi MACSQuant 10 Analyzer. Representative gating strategies are presented in Supplementary Fig. S1. To determine absolute cell number per gram of tumor, total numbers of cells in appropriate gates were multiplied by a correction factor for the proportion of the tumor sample run through the cytometer, and normalized for total tumor weight.
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