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7 protocols using lightning link apc conjugation kit

1

Isolation and Characterization of Neuronal Nuclei

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Antibodies against nuclear proteins, as well as isotype-matched control IgGs, were preconjugated to Allophycocyanin (APC) using lightning-link APC conjugation kit (Innova Biosciences). The monoclonal antibody against NeuN coupled to Alexa-Fluor 488 (Millipore, MAB 477X) was used for neuron-specific labeling. The antibodies and reagents used in this study are listed in Supplementary Table 3. Approximately 1–2 μg of antibody was added to1×106 nuclei/ml and incubated at 4°C for 12 hrs with gentle rocking in the dark. Labeled nuclei were washed twice by centrifugation and filtered to remove clumps before performing FACS. The DNA binding dyes DAPI or propidium iodide were used for gating of nuclei. Aggregate discrimination was achieved based on the height, area and width parameters for front scattering (FSC) and side scattering (SSC). The purity and identity of isolated neuronal nuclei was further confirmed by microscopy and epigenetic analysis. For each antibody, the geometric mean value of single-nuclei events that is above the matched nonspecific IgG control was determined. An average of 10,000 events was acquired for FACS analysis. For ChIP assays, ~1×106 FACS-sorted neuronal nuclei were collected by centrifugation.
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2

Isolation and Characterization of Neuronal Nuclei

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Antibodies against nuclear proteins, as well as isotype-matched control IgGs, were preconjugated to Allophycocyanin (APC) using lightning-link APC conjugation kit (Innova Biosciences). The monoclonal antibody against NeuN coupled to Alexa-Fluor 488 (Millipore, MAB 477X) was used for neuron-specific labeling. The antibodies and reagents used in this study are listed in Supplementary Table 3. Approximately 1–2 μg of antibody was added to1×106 nuclei/ml and incubated at 4°C for 12 hrs with gentle rocking in the dark. Labeled nuclei were washed twice by centrifugation and filtered to remove clumps before performing FACS. The DNA binding dyes DAPI or propidium iodide were used for gating of nuclei. Aggregate discrimination was achieved based on the height, area and width parameters for front scattering (FSC) and side scattering (SSC). The purity and identity of isolated neuronal nuclei was further confirmed by microscopy and epigenetic analysis. For each antibody, the geometric mean value of single-nuclei events that is above the matched nonspecific IgG control was determined. An average of 10,000 events was acquired for FACS analysis. For ChIP assays, ~1×106 FACS-sorted neuronal nuclei were collected by centrifugation.
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3

Multiparametric Flow Cytometry Analysis

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Flow cytometry was applied to analyze the cell surface molecule expression and intracellular cytokine expression. The antibodies used were as follows: FITC-conjugatedanti-mouse CD4; F4/80; TNF-α; IFN-γ; anti-human CD14; eFluor® 488-conjugated anti-mouse TNF-α; PE-conjugated anti-mouse CD8; Tim-3; TGF-β1; IL-10; anti-human Tim-3; PerCP/Cy5.5-conjugated anti-mouse IL-17A; PE/CY7-conjugated anti-mouse F4/80; IL-10; TNF-α; IL-12/23; APC-conjugated anti-mouse F4/80; Tim-3; TNF-α; IL-10; Brilliant Violet 421-conjugated anti-mouse TGF-β1; CD206; TNF-α; IL-4; Brilliant Violet 510-conjugated anti-mouse CD86; TNF-α; CD4; Brilliant Violet 605-conjugated anti-mouse IL-17A; CD4 (Biolegend, San Diego, CA, USA). The HIF-2α antibody (Santa Cruz, CA, USA) was pretreated with the Lightning-Link APC Conjugation Kit (Innova Biosciences, Cambridge, UK). Before intracellular staining, a Fix/Perm kit (Biolegend, San Diego, CA, USA) was used to fix and permeabilize cells. Flow cytometry was carried out using a Beckman-Coulter CyAn ADP cytometer (Beckman-Coulter, Bria, CA, USA) and analyzed using FlowJo software (Tree Star, Ashland, OR, USA).
The production of Angiopoietin-2, EGF, FGF, TGF-α, PDGF-AA, PDGF-BB, and VEGF by EVTs was evaluated using a Multi-Analyte Flow Assay Kit (Human Growth Factor Panel, Biolegend, San Diego, CA, USA).
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4

APC Conjugation of Immunomodulatory Proteins

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APC‐conjugated proteins: PD‐1‐Ig (Bio‐Techne, 1086‐PD‐050), anti‐PD‐L1 (Durvalumab) and CTLA‐4 Ig (Abatacept & Belatacept) were generated using the APC Conjugation Kit—Lightning‐Link® according to manufacturer's instructions (Abcam, ab201807). APC‐conjugated anti‐PD‐L1 antibodies were procured from ThermoFisher (clone MIH1 [#14‐5983‐82]), or Biolegend (clones MIH3 [#374513] and 29E.2A3 [#329707]). Anti CD28‐APC was procured from BD Biosciences (#559770).
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5

Comprehensive T Cell Phenotyping

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Changes in T cell phenotype by flow cytometry were performed to analyze activation and memory surface markers before and after T cell encapsulation using BD Accuri C6 Plus equipment (BD Bioscience, Franklin Lakes, NY, USA). Three and four multicolor flow cytometry panels were employed to study the T cell phenotype changes. Zombie NIR fixable cell viability dye (BioLegend, San Diego, CA, USA) was used to discriminate the dead cell population in both panels. To identify the activated T cell populations, APC-CD8, PE-CD69, and Kiravia blue HLA-DR labeled antibodies (BioLegend, San Diego, CA, USA) were employed. Similar to the activation panel, the memory panel also included APC-CD8 along with FITC-CD45RA labeled antibody (BioLegend, San Diego, CA, USA). In both panels, labeled antibodies were employed according to the manufacturer's instructions at 5 μl antibodies per 1 M cells in a 100 μL sample. Moreover, the CAR content of the T cell population was identified using 400 ng/106 T cells of 1A7 anti-14G2a idiotype antibody (Absolute Antibody, Boston, MA, USA) conjugated with APC Conjugation Kit – Lightning-Link (Abcam, Waltham, MA, USA). The 1A7 anti-14G2a idiotype antibody was employed along with FITC-CD8 labeled antibody to form 3 panels with PE-CD45RA, PE-CD45RO, and PE-HLADR (BioLegend, San Diego, CA, USA) for the CAR-cell phenotype characterization.
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6

SARS-CoV-2 Spike and RBD Staining of PBMCs

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PBMCs were stained with SARS-CoV-2 Spike and RBD probes, as previously described (Juno et al., 2020 (link)). Probes were generated by sequential addition of streptavidin-phycoerythrin (PE) (Thermo Fisher Scientific) to trimeric S protein biotinylated using recombinant Bir-A (Avidity), while SARS-CoV-2 RBD was labeled to APC using an APC Conjugation Lightning-Link Kit (Abcam). PBMCs were surface stained with Aqua viability dye (Thermo Fisher) and monoclonal antibodies against CD19-ECD (#IM2708U, Beckman Coulter), IgM BUV395 (#563903), CD21 BUV737 (#564437), IgD PE-Cy7 (#561314), IgG BV786 (#564230), streptavidin-BV510 (#563261) (BD Biosciences), CD20 APC-Cy7 (#302314), CD14 BV510 (#301841), CD3 BV510 (#317332), CD8a BV510 (#301048), CD16 BV510 (#302048), CD10 BV510 (#312220) and CD27 BV605 (#302829) (BioLegend). Cells were washed, fixed with 1% formaldehyde and acquired on a BD LSRII Fortessa.
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7

Workflow for SARS-CoV-2 S-specific B Cell Profiling

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Probes for delineating SARS-CoV-2 S-specific B cells within cryopreserved human PBMC were generated by sequential addition of streptavidin-PE (Thermofisher) to trimeric S protein biotinylated using recombinant Bir-A (Avidity). SARS-CoV-2 RBD protein was directly labelled to APC using an APC Conjugation Lightning-link kit (Abcam). Cells were stained with Aqua viability dye (Thermofisher). Monoclonal antibodies for surface staining included: CD19-ECD (J3-119) (Beckman Coulter), CD20 Alexa700 (2H7), IgM-BUV395 (G20-127), CD21-BUV737 (B-ly4), IgD-Cy7PE (IA6-2), IgG-BV786 (G18-145) (BD), CD14-BV510 (M5E2), CD3-BV510 (OKT3), CD8a-BV510 (RPA-T8), CD16-BV510 (3G8), CD10-BV510 (HI10a), CD27-BV605 (O323) (Biolegend), IgA-Vio450 (clone) (Miltenyi). Cells were washed, fixed with 1% formaldehyde (Polysciences) and acquired on a BD LSR Fortessa or BD Aria II. Gating is shown in Supplementary Fig. 4.
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