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11 protocols using anti cd19 percp cy5

1

Multiparametric Flow Cytometry Analysis of Immune Cell Subsets

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The subsets of T lymphocytes14 (link),15 (link) and monocytes12 (link),13 (link) at baseline and at following timepoints during PU-H71 treatment were monitored by flow cytometry. Peripheral blood (PB) cells from healthy donor was used as a control. Cells were isolated by the Ficoll-Paque method from PB and bone marrow (BM) aspirates. Cells were labeled with anti-CD45 APC-H7, anti-CD33 BV650 (BD Biosciences, clone WM53, cat. 303430), anti-CD56 AlexaFluor700 (BioLegend, clone HCD56, cat. 318316), anti-CD3 BV711 (BioLegend, clone SK7, cat. 344838), anti-CD4 PE-Cy5 (BioLegend, clone OKT4, cat. 317412), anti-CD8 BV605 (BioLegend, clone SK1, cat. 344742), anti-CD19 PerCP/Cy5.5 (BioLegend, clone HIB19, cat. 302230), anti-CD14 PE (BD Biosciences, clone M5E2, cat. 555398), anti-CD16 BV785 (BioLegend, clone 3G8, cat. 302046), anti-CD45RA PE-Cy7 (BioLegend, clone HI100, cat. 304126) and anti-CCR7 Alexa Fluor 647 (BD Biosciences, clone 150503, cat. 560816). After washing, flow cytometry evaluation was performed on BD LSRFortessa. Data was analyzed using FlowJo software.
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2

Comprehensive Immune Cell Phenotyping

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Mice were anesthetized with tribromoethanol, and perfused via the left
ventricle with cold PBS. Brains were then harvested and cells were collected
using the Miltenyi Neural dissociation kit (San Diego, CA). Cells were then
blocked with Anti CD16/CD32 (15 min, 4 °C). Cells were then stained with
the following monoclonal antibodies at 4 °C for 45 min: Anti-CD11b PE,
anti-CD8 Pac Blue, anti-CD19 Percp-cy5.5, anti-CD4 Pe-cy7, anti CD45
PE-Dazzle594, anti-CD86 FITC, anti-CD45 Alexa Flour 700, anti-Ly6G PE,
anti-CD11c Pacific Blue, anti-MHC II Percpcy5.5, anti-CD11b Bv650 all purchased
from Biolegend (San Diego, CA), and anti-Ly6C PEtxRed (BD Biosciences, San Jose,
CA), anti-F4/80 APC-cy7, anti-O4 Alexa Flour 488 (R & D Systems),
anti-ASCA-2 APC (Miltenyi), anti-CD3 V500 (BD Biosciences), and anti-CD192 APC
(R & D Systems, Minneapolis, MN). Cells were then fixed, permeabilized,
(Fixation Buffer and Permeabilization wash buffer; Biolegend) and stained with
intracellular stains anti-CD68 PEcy7 (Biolegend), anti-NeuN Alexa Flour 700
(Novus Biologicals, Littleton, CO) (4 °C 45 min). Cells were then washed
twice and resuspended. Samples were run on an LSRFORTESSA flow cytometer (BD
Biosciences). Data was analyzed with Flowjo v10.1 (Flowjo, Ashland, OR).
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3

Flow Cytometry Analysis of Macrophages

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Flow cytometry analysis of nontargeting control and siGAPLINC-treated MDMs stained with CD11B FITC (Thermo Fisher), CD16 PE (Thermo Fisher), and CD14 FITC (Biolegend).
Blood was collected immediately postmortem by cardiac puncture, and single-cell suspensions prepared from the spleen of WT and Gaplinc-KO mice were depleted of red blood cells (RBCs) prior to staining. Fragment, crystallizable (Fc) receptors were blocked (anti-CD16/32, BD Pharmingen) prior to staining with LIVE/DEAD Fixable Aqua Dead Cell Stain (Thermo Fisher), anti–CD11b-AlexaFluor 700, anti–LY6G-BV421, anti–LY6C-AlexaFluor 488, anti–CD19 PerCP-Cy5.5, anti–CSF-1R APC (BioLegend), anti–CD3-PE (BD), anti–SiglecF BV650 (BD OptiBuild), and anti–F4/80 PE-eFluor 610 (eBioScience).
Flow cytometry analysis of peritoneal fluid isolated from WT and Gaplinc-KO mice (24 (link)) challenged with LPS i.p. for 18 h was performed; cells were stained with anti–CD11b-AlexaFluor 700 and anti–F4/80 PE-eFluor 610 (eBioScience).
Flow cytometry analysis of BMDMs harvested from WT and Gaplinc-KO mice was performed; cells were stained with anti–CD11b-AlexaFluor 700 and anti–F4/80 PE-eFluor 610 (eBioScience).
Data acquisition was performed using Attune NxT (Thermo Fisher). Analysis was performed using FlowJo analysis software (BD Biosciences).
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4

Sorting SARS-CoV-2 Spike-Specific B Cells

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Fluorescence-activated cell sorting of cryopreserved PBMCs was performed on a BD FACS Melody. Sorting baits (SARS-CoV-2 Spike) was pre-complexes with the streptavidin flurophore at a 1:4 molar ratio prior to addition to cells. PBMCs were stained with live/dead (fixable Aqua Dead, Thermofisher), anti-CD3-APC/Cy7 (Biolegend), anti-CD8-APC-Cy7 (Biolegend), anti-CD14-BV510 (Biolegend), anti-CD19-PerCP-Cy5.5 (Biolegend), anti-IgM-PE (Biolegend), anti-IgD-Pacific Blue (Biolegend) and anti-IgG-PeCy7 (BD) and Spike-Alexa488 (Thermofisher Scientific, S32354) and Spike-APC (Thermofisher Scientific, S32362). Live CD3/CD8CD14CD19+IgMIgDIgG+Spike+Spike+ cells were sorted into individual wells containing RNase OUT (Invitrogen), First Strand SuperScript III buffer, DTT and H2O (Invitrogen) and RNA was converted into cDNA (SuperScript III Reverse Transcriptase, Invitrogen) using random hexamers following the manufacturer’s protocol.
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5

Comprehensive Immune Cell Profiling

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Single cell suspensions from IEL and LP were labelled with a cocktail of flurochrome conjugated antibodies against surface antigens purchased from either BD Biosciences (San Jose, CA) or Biolegend (San Diego, CA): anti-CD45 FITC, anti-CD19 PerCP Cy5.5, anti-Siglec H Pacific Blue, anti-I/A I/E BV605, anti-CD11b BV 650, anti-CD3e BV786, anti-B220 BUV496, anti-EpCam APC, anti-F4/80 AF700, anti-Ly6c APC-Cy7, anti-CD11c PE-CF594, anti-CD103 PE-Cy7 and Zombie aqua kit. Cells were fixed with 1% PFA prior to acquisition in Flow Cytometry. Cells were acquired using a 18 color BD LSRFortessa (San Jose, CA) and analyzed with FlowJO software (Ashland, Oregon).
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6

Detailed PBMC Subset Analysis

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The purified PBMCs were resuspended in a complete RPMI-1640 medium (HyClone) and then incubated on the 96-well plate at a concentration of 1×106 cells/well. The cells were washed once with phosphate-buffered saline (PBS), and fixed and permeabilized using a fixation/permeabilisation kit (BD Biosciences, San Diego, CA, USA). For surface staining, after fixation and permeabilization, the cells were stained with the antibody cocktail: anti-CD19 PerCP/Cy5.5, anti-CD24 PE, anti-CD27 PE/Cy7, and anti-CD38 APC; Biolegend, San Diego, CA, USA. The cells were incubated for 1 hour in the dark and washed twice with 200 µL of PBS containing 0.5% bovine serum albumin. After discarding the supernatant, cells were resuspended in 300 µL of PBS for flow cytometry. Samples were detected by flow cytometry on a FACS Verse flow cytometer (BD Biosciences), which was followed by analysis with FlowJo 10.1 software (Tree Star, San Carlos, CA, USA). At least 50,000 events per sample were analyzed. Cells stained with isotype control antibody served as the negative control. Compensation was made according to single staining. The cells were gated initially for living lymphocytes as CD19+ using forward and side scatter histogram. The expression of CD19+CD24hiCD38hi B cells, CD19+CD24hiCD27+ B cells, CD19+CD27+ B cells, CD19+CD27 B cells, and CD19+CD38+CD24 plasma cells were detected separately.
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7

Quantifying B Cell Subpopulations

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All fresh samples were transported at 4°C. Peripheral blood samples were mixed with an equal volume of 0.9% NaCl and centrifuged at 800g for 20 min using a Lymphoprep separation solution (Axis-Shield, Norway) to obtain peripheral blood mononuclear cells. The next steps were performed using previously published protocols (25 (link)). Briefly, B cells were labeled with various antibodies [NR1-FITC, OriGene; anti-CD19-percp/Cy5.5, Biolegend; LGI1-green fluorescent protein (GFP), our lab] and 4′,6-diamidino-2-phenylindole for sorting and counting. FlowJo software (version 10.7) was used for quantitative analysis of the flow cytometry, and the numbers of NR1-positive and LGI-positive B cells were calculated in 100,000 peripheral blood mononuclear cells from each sample.
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8

SARS-CoV-2 Antigen-Specific B Cell Sorting

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Fluorescence-activated cell sorting of cryopreserved PBMCs was performed on a BD FACS Melody as previously described (Graham et al., 2021 (link)). Sorting baits (SARS-CoV-2 Spike and RBD) was pre-complexed with the streptavidin fluorophore at a 1:4 molar ratio prior to addition to cells. PBMCs were stained with live/dead (fixable Aqua Dead, Thermofisher), anti-CD3-APC/Cy7 (Biolegend), anti-CD8-APC-Cy7 (Biolegend), anti-CD14-BV510 (Biolegend), anti-CD19-PerCP-Cy5.5 (Biolegend), anti-IgM-PE (Biolegend), anti-IgD-Pacific Blue (Biolegend) and anti-IgG-PeCy7 (BD) and Spike-Alexa488 (Thermofisher Scientific, S32354) and Spike-APC (Thermofisher Scientific, S32362) or RBD-Alexa488 and RBD-APC. Live CD3/CD8-CD14-CD19+IgM-IgD-IgG+Spike+Spike+ or CD3/CD8-CD14-CD19+IgM-IgD-IgG+RBD+RBD+ cells were sorted using a BD FACS Melody into individual wells containing RNase OUT (Invitrogen), First Strand SuperScript III buffer, DTT and H2O (Invitrogen) and RNA was converted into cDNA (SuperScript III Reverse Transcriptase, Invitrogen) using random hexamers (Bioline Reagents Ltd) following the manufacturer’s protocol.
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9

Comprehensive Immune Cell Profiling

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B- and T-cell subsets were enumerated in freshly thawed cryopreserved PBMCs. After washing and counting viable cells, PBMCs were surface-stained with the following conjugated mAbs: anti-CD3-AF488 (Biolegend; clone HIT3a), anti CD8-APC/Cy7 (Biolegend; SK1), anti-CD19-APC/Cy7 (BD Biosciences; SJ25C1), anti-CD19-PerCP/Cy5.5 (Biolegend; HiB19) anti-CD25-PE/Cy7 (Biolegend; BC96), anti-CD21-PE/Cy7 (BD Biosciences; B-ly4), anti-CD27-PerCP/Cy5.5 (BD Biosciences; M-T271), anti-CD38-PE/Cy7 (Biolegend; HIT2), anti-HLA-DR-PerCP/Cy5.5 (Biolegend; L243); anti-CD10-FITC (BD Biosciences; W8E7), anti-IL21R-PE (BD Biosciences; 17A12), and anti-CD39-APC (Biolegend; A1). Cells were fixed and permeabilized with Cytofix/Cytoperm (BD Biosciences), and stained with anti-IL-10-PE (R & D Systems; 127107), anti-FOXP3-PE (Biolegend; 206D) and anti- TGFβ-PE (Biolegend; TW4-2F8), and analyzed with Guava easyCyte 8HT and FlowJo (Treestar). Subsets were expressed as percentages of the parent CD4+, CD8+ and CD19+ cell populations. The gating strategy is presented in S2 Fig.
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10

Multicolor Flow Cytometry Analysis of Liver and Spleen Lymphocytes

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Lymphocytes from the liver and spleen of mice were isolated as previously described23 (link) and analyzed by multicolor flow cytometry. Flow cytometry was performed on a CytoFLEX LX platform and results were analyzed using FlowJo software. The following antibodies were used in this study (clone, manufacture): anti-F4/80-Alexa Fluor 700 (BM8, BioLegend), anti-B220-Alexa Fluor 700 (RA3-6B2, BioLegend), anti-Cd11b-Alexa Fluor 700 (M1/70, BioLegend), anti-Cd3-Alexa Fluor 594 (17A2, BioLegend) anti-Cd4-BV605 (GK1.5, BioLegend), anti-Cd8-BV786 (53-6.7, BD), anti-Foxp3-BV421 (MF-14, BioLegend), anti-Cd62l-PerCP/Cy5.5 (MEL-14, BioLegend), anti-Cd44-BV510 (IM7, BioLegend), anti-NK1.1-BV510 (PK136, BioLegend), anti-A2Ar-FITC (7F6-G5-A2, NOVUS), anti-Cd73-APC (TY11.8, BioLegend), anti-Cd39-PECy7 (Duha59, BioLegend), anti-Cd19-PerCP Cy5.5(6D5, BioLegend), anti-PD1-APC/Cy7 (29F.1A12, BioLegend), anti-Cd107a- PE (1D4B, BD), anti-CD69-BV650 (H1.2F3, BioLegend), anti-Ifnγ-BV421 (XMG1.2, BioLegend), anti-Tnfα-PerCPCy5.5 (MP6-XT22, BioLegend), anti-GZMB-FITC (GB11, BioLegend), and anti-perforin-APC (S16009A, BioLegend).
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