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3 protocols using cd18 pe

1

Evaluating Dendritic Cell Surface Markers

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Expression of DC surface markers was evaluated by LSR-II cytometer (BD Bioscience) using the following antibodies: anti-MHC class II-PE-Cy7 (#107629/BioLegend) or APC-Cy7 (#107628/BioLegend) anti-CD11c-FITC (#117306/BioLegend) or PerCP-Cy5.5 (#560584/BD Pharmingen), anti-CD86-PerCP (#105025/BioLegend), anti-CD40-Pacific Blue (#124626/BioLegend), anti-PD-DL-1-Qdot-605 (#124321/BioLegend), ICAM-1-FITC (#11054182/eBioscience), CD18-PE (#101408/BioLegend), CD69-PE-Cy7 (#25069182/eBioscience), CD11a-APC (#101120/BioLegend), CD44-e450 (#48044182/eBioscience), CD11b BV605 (#83011242/eBioscience; all used in 1:100 dilution), and anti-AXL-APC (#FAB8541A/R&D Systems; dilution 1:20). The dead cells were excluded with Fixable Viability Dye eFluor 780 or e506 (#650866/ThermoFisher Scientfic). There was no difference in viable cell proportion of BM-derived DCs between WT and miR-34a−/− genotypes (mean±s.d: 75% ±12 and 71% ±10, respectively).
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2

CXCR4 and CD18 Single-Cell RNA Sequencing

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Forty million HG3 cells from the bulk TP0 and TP1 populations were co-stained using human CXCR4-APC (1:10 dilution, Thermo Fisher Scientific, FAB173A) and CD18-PE (1:100 dilution, BioLegend, 302108) conjugated antibodies. CXCR4 and CD18 single-positive cells (representative of HS and LS subpopulations) were isolated using a BD FACSAria II. Three biological replicates were collected over a 2-week period. RNA was isolated using a RNeasy Micro kit (QIAGEN, 74004) and RNA quality was verified using an Agilent Bioanalyzer Pico Eukaryote chip. Then, 400 ng of total RNA was used as input for library preparation using the KAPA stranded mRNA HyperPrep kit (KAPA Biosystems, KK8580) per the manufacturer’s instructions. Library yields and sizes were confirmed using an Agilent High Sensitivity DNA kit (Agilent Technologies, 5067–4626) on an Agilent 2100 bioanalyzer. Libraries were pooled in equimolar ratios and sequenced using a 75-cycle high output kit on an Illumina NextSeq 500 system. Bulk RNA sequencing data for 23 fludarabine and 13 ibrutinib-treated patients were from dbGaP (accession numbers phs000922.v1.p1 and phs001431.v1.p, respectively).
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3

Monocyte Phenotyping by Flow Cytometry

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All flow cytometry tests were performed on freshly prepared PBMCs and CD14 þ CD16 -monocytes. After blocking nonspecific antibody binding with human TruStain FcX (BioLegend, USA), the following monoclonal antibodies were used for flow cytometry: CD14-FITC, CD16-BV421, CCR1-PE, CCR2-PE/Cy7, CCR5-APC, CD11b-APC, CD18-PE (all from BioLegend, USA). We performed compensation using CompBeads (Becton Dickinson, USA). Flow cytometric analysis was performed on the CytoFLEX platform (Beckman Coulter, USA). The acquired data were analyzed by FlowJo software (Becton Dickinson, USA). Unstained monocytes were used as a negative control. Monocytes in PBMCs were identified as HLA-DR þ CD3 À CD19 -population with the unique forward and side-scatter properties.
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