Binding Assay:
Article Title: Multi-antigen-targeting T cells in pediatric central nervous system tumors: a phase 1 trial.
Article Snippet: Following incubation, cells were washed by adding 2 ml of MACSQuant Running Buffer (Miltenyi Biotec, cat. no. 130-092-747) and centrifuged at 400g for 5 min, and then resuspended in 100 μl of MACSQuant Running Buffer. .. An FcR blocking agent (Miltenyi Biotec, cat. no. 130-059-901) was added to the tubes for 5 min to prevent any nonspecific binding, followed by an appropriate antibody mix (shown in tables below), which was incubated in the dark for 15 min. Antibodies for the pan leukocyte panel included CD14 Vio Blue (Miltenyi Biotec, cat. no. 130-110-524), CD19 FITC (Miltenyi Biotec, cat. no. 130-113-646), CD16 PE (Miltenyi Biotec, cat. no. 130-113-393), CD56 PE (Miltenyi Biotec, cat. no. 130-113-312), CD3 Per CP Vio-770 (Miltenyi Biotec, cat. no. 130-113-141), CD4 PE-Vio-770 (Miltenyi Biotec, cat. no. 130-113-227), CD45 APC (Miltenyi Biotec, cat. no. 130-110-633) and CD8 APC Vio-770 (Miltenyi Biotec, cat. no. 130-110-681). .. Antibodies for the TCR/DC panel included TCRγδ Vio Blue (Miltenyi Biotec, cat. no.1 30-119-619), TCRαβ FITC (Miltenyi Biotec, cat. no. 130-113-538), CD83 PE (Miltenyi Biotec, cat. no. 130-110-503), CD3 Per CP Vio-770 (Miltenyi Biotec, cat. no. 130-113-141) and CD45 APC (Miltenyi Biotec, cat. no. 130-110-633).
Blocking Assay:
Article Title: Topoisomerase III-beta protects from immune dysregulation and tumorigenesis
Article Snippet: Cells were incubated with Live/Dead fixable Aqua dead cell stain kit (Invitrogen, #L34957). .. Before antibody staining, cells were blocked using Fc receptor blocking agent, mouse (Miltenyi Biotec, #130-092-575), followed by incubation with antibodies for surface staining for 20 min at 4°C. .. The antibodies used were CD4 (RM4-5, BioLegend, #100542), CD8 (53-6.7, BioLegend, #100733), CD3 (17A2, BioLegend, #100237), CD11b (1D3/39, BioLegend, #152408), CD11c (N418, BioLegend, #117310), Ly6C (HK1.4, BioLegend, #128031), Ly6G (1A8, BioLegend, #127618), major histocompatibility complex class II (REA813, Miltenyi, #130-112-391), CD45 (30-F11, BioLegend, #103151), and CD19 (1D3/CD19, BioLegend, #152413).
Article Title: Multi-antigen-targeting T cells in pediatric central nervous system tumors: a phase 1 trial.
Article Snippet: Following incubation, cells were washed by adding 2 ml of MACSQuant Running Buffer (Miltenyi Biotec, cat. no. 130-092-747) and centrifuged at 400g for 5 min, and then resuspended in 100 μl of MACSQuant Running Buffer. .. An FcR blocking agent (Miltenyi Biotec, cat. no. 130-059-901) was added to the tubes for 5 min to prevent any nonspecific binding, followed by an appropriate antibody mix (shown in tables below), which was incubated in the dark for 15 min. Antibodies for the pan leukocyte panel included CD14 Vio Blue (Miltenyi Biotec, cat. no. 130-110-524), CD19 FITC (Miltenyi Biotec, cat. no. 130-113-646), CD16 PE (Miltenyi Biotec, cat. no. 130-113-393), CD56 PE (Miltenyi Biotec, cat. no. 130-113-312), CD3 Per CP Vio-770 (Miltenyi Biotec, cat. no. 130-113-141), CD4 PE-Vio-770 (Miltenyi Biotec, cat. no. 130-113-227), CD45 APC (Miltenyi Biotec, cat. no. 130-110-633) and CD8 APC Vio-770 (Miltenyi Biotec, cat. no. 130-110-681). .. Antibodies for the TCR/DC panel included TCRγδ Vio Blue (Miltenyi Biotec, cat. no.1 30-119-619), TCRαβ FITC (Miltenyi Biotec, cat. no. 130-113-538), CD83 PE (Miltenyi Biotec, cat. no. 130-110-503), CD3 Per CP Vio-770 (Miltenyi Biotec, cat. no. 130-113-141) and CD45 APC (Miltenyi Biotec, cat. no. 130-110-633).
Article Title: Topoisomerase III-beta protects from immune dysregulation and tumorigenesis.
Article Snippet: Cells were incubated with Live/Dead fixable Aqua dead cell stain kit (Invitrogen, #L34957). .. Before antibody staining, cells were blocked using Fc receptor blocking agent, mouse (Miltenyi Biotec, #130- 092- 575), followed by incubation with antibodies for surface staining for 20 min at 4°C. .. The antibodies used were CD4 (RM4- 5, BioLegend, #100542), CD8 (53- 6.7, BioLegend, #100733), CD3 (17A2, BioLegend, #100237), CD11b (1D3/39, BioLegend, #152408), CD11c (N418, BioLegend, #117310), Ly6C (HK1.4, BioLegend, #128031), Ly6G (1A8, BioLegend, #127618), major histocompatibility complex class II (REA813, Miltenyi, #130- 112- 391), CD45 (30- F11, BioLegend, #103151), and CD19 (1D3/ CD19, BioLegend, #152413).
Article Title: Apolipoprotein E drives microglia activation in the development of autoimmune uveitis through up-regulation of peptidyl prolyl isomerase F
Article Snippet: .. For surface receptor staining, the prepared cell suspension was treated with a mouse Fc receptor blocking agent (Miltenyi Biotec, 130-092-575, diluted 1:100) and incubated at 4°C for 20 min, followed by staining with specific antibodies at 4°C in the dark for 20 min. .. Cells were then fixed and permeabilized using a flow cytometry fixation/permeabilization buffer (Thermo Fisher Scientific, 00-5223-56 and 00-5123-43) at room temperature in the dark for 10 min. For intracellular cytokine staining, the cells were subsequently incubated with a flow cytometry permeabilization buffer (Thermo Fisher Scientific, 00-8333-56), followed by the addition of specific antibodies and incubation at room temperature in the dark for 20 min. Acquisition and compensation were performed by Cytek Aurora Spectral Flow Cytometry.
Incubation:
Article Title: Topoisomerase III-beta protects from immune dysregulation and tumorigenesis
Article Snippet: Cells were incubated with Live/Dead fixable Aqua dead cell stain kit (Invitrogen, #L34957). .. Before antibody staining, cells were blocked using Fc receptor blocking agent, mouse (Miltenyi Biotec, #130-092-575), followed by incubation with antibodies for surface staining for 20 min at 4°C. .. The antibodies used were CD4 (RM4-5, BioLegend, #100542), CD8 (53-6.7, BioLegend, #100733), CD3 (17A2, BioLegend, #100237), CD11b (1D3/39, BioLegend, #152408), CD11c (N418, BioLegend, #117310), Ly6C (HK1.4, BioLegend, #128031), Ly6G (1A8, BioLegend, #127618), major histocompatibility complex class II (REA813, Miltenyi, #130-112-391), CD45 (30-F11, BioLegend, #103151), and CD19 (1D3/CD19, BioLegend, #152413).
Article Title: Multi-antigen-targeting T cells in pediatric central nervous system tumors: a phase 1 trial.
Article Snippet: Following incubation, cells were washed by adding 2 ml of MACSQuant Running Buffer (Miltenyi Biotec, cat. no. 130-092-747) and centrifuged at 400g for 5 min, and then resuspended in 100 μl of MACSQuant Running Buffer. .. An FcR blocking agent (Miltenyi Biotec, cat. no. 130-059-901) was added to the tubes for 5 min to prevent any nonspecific binding, followed by an appropriate antibody mix (shown in tables below), which was incubated in the dark for 15 min. Antibodies for the pan leukocyte panel included CD14 Vio Blue (Miltenyi Biotec, cat. no. 130-110-524), CD19 FITC (Miltenyi Biotec, cat. no. 130-113-646), CD16 PE (Miltenyi Biotec, cat. no. 130-113-393), CD56 PE (Miltenyi Biotec, cat. no. 130-113-312), CD3 Per CP Vio-770 (Miltenyi Biotec, cat. no. 130-113-141), CD4 PE-Vio-770 (Miltenyi Biotec, cat. no. 130-113-227), CD45 APC (Miltenyi Biotec, cat. no. 130-110-633) and CD8 APC Vio-770 (Miltenyi Biotec, cat. no. 130-110-681). .. Antibodies for the TCR/DC panel included TCRγδ Vio Blue (Miltenyi Biotec, cat. no.1 30-119-619), TCRαβ FITC (Miltenyi Biotec, cat. no. 130-113-538), CD83 PE (Miltenyi Biotec, cat. no. 130-110-503), CD3 Per CP Vio-770 (Miltenyi Biotec, cat. no. 130-113-141) and CD45 APC (Miltenyi Biotec, cat. no. 130-110-633).
Article Title: Topoisomerase III-beta protects from immune dysregulation and tumorigenesis.
Article Snippet: Cells were incubated with Live/Dead fixable Aqua dead cell stain kit (Invitrogen, #L34957). .. Before antibody staining, cells were blocked using Fc receptor blocking agent, mouse (Miltenyi Biotec, #130- 092- 575), followed by incubation with antibodies for surface staining for 20 min at 4°C. .. The antibodies used were CD4 (RM4- 5, BioLegend, #100542), CD8 (53- 6.7, BioLegend, #100733), CD3 (17A2, BioLegend, #100237), CD11b (1D3/39, BioLegend, #152408), CD11c (N418, BioLegend, #117310), Ly6C (HK1.4, BioLegend, #128031), Ly6G (1A8, BioLegend, #127618), major histocompatibility complex class II (REA813, Miltenyi, #130- 112- 391), CD45 (30- F11, BioLegend, #103151), and CD19 (1D3/ CD19, BioLegend, #152413).
Article Title: Apolipoprotein E drives microglia activation in the development of autoimmune uveitis through up-regulation of peptidyl prolyl isomerase F
Article Snippet: .. For surface receptor staining, the prepared cell suspension was treated with a mouse Fc receptor blocking agent (Miltenyi Biotec, 130-092-575, diluted 1:100) and incubated at 4°C for 20 min, followed by staining with specific antibodies at 4°C in the dark for 20 min. .. Cells were then fixed and permeabilized using a flow cytometry fixation/permeabilization buffer (Thermo Fisher Scientific, 00-5223-56 and 00-5123-43) at room temperature in the dark for 10 min. For intracellular cytokine staining, the cells were subsequently incubated with a flow cytometry permeabilization buffer (Thermo Fisher Scientific, 00-8333-56), followed by the addition of specific antibodies and incubation at room temperature in the dark for 20 min. Acquisition and compensation were performed by Cytek Aurora Spectral Flow Cytometry.
Staining:
Article Title: Topoisomerase III-beta protects from immune dysregulation and tumorigenesis
Article Snippet: Cells were incubated with Live/Dead fixable Aqua dead cell stain kit (Invitrogen, #L34957). .. Before antibody staining, cells were blocked using Fc receptor blocking agent, mouse (Miltenyi Biotec, #130-092-575), followed by incubation with antibodies for surface staining for 20 min at 4°C. .. The antibodies used were CD4 (RM4-5, BioLegend, #100542), CD8 (53-6.7, BioLegend, #100733), CD3 (17A2, BioLegend, #100237), CD11b (1D3/39, BioLegend, #152408), CD11c (N418, BioLegend, #117310), Ly6C (HK1.4, BioLegend, #128031), Ly6G (1A8, BioLegend, #127618), major histocompatibility complex class II (REA813, Miltenyi, #130-112-391), CD45 (30-F11, BioLegend, #103151), and CD19 (1D3/CD19, BioLegend, #152413).
Article Title: Topoisomerase III-beta protects from immune dysregulation and tumorigenesis.
Article Snippet: Cells were incubated with Live/Dead fixable Aqua dead cell stain kit (Invitrogen, #L34957). .. Before antibody staining, cells were blocked using Fc receptor blocking agent, mouse (Miltenyi Biotec, #130- 092- 575), followed by incubation with antibodies for surface staining for 20 min at 4°C. .. The antibodies used were CD4 (RM4- 5, BioLegend, #100542), CD8 (53- 6.7, BioLegend, #100733), CD3 (17A2, BioLegend, #100237), CD11b (1D3/39, BioLegend, #152408), CD11c (N418, BioLegend, #117310), Ly6C (HK1.4, BioLegend, #128031), Ly6G (1A8, BioLegend, #127618), major histocompatibility complex class II (REA813, Miltenyi, #130- 112- 391), CD45 (30- F11, BioLegend, #103151), and CD19 (1D3/ CD19, BioLegend, #152413).
Article Title: Apolipoprotein E drives microglia activation in the development of autoimmune uveitis through up-regulation of peptidyl prolyl isomerase F
Article Snippet: .. For surface receptor staining, the prepared cell suspension was treated with a mouse Fc receptor blocking agent (Miltenyi Biotec, 130-092-575, diluted 1:100) and incubated at 4°C for 20 min, followed by staining with specific antibodies at 4°C in the dark for 20 min. .. Cells were then fixed and permeabilized using a flow cytometry fixation/permeabilization buffer (Thermo Fisher Scientific, 00-5223-56 and 00-5123-43) at room temperature in the dark for 10 min. For intracellular cytokine staining, the cells were subsequently incubated with a flow cytometry permeabilization buffer (Thermo Fisher Scientific, 00-8333-56), followed by the addition of specific antibodies and incubation at room temperature in the dark for 20 min. Acquisition and compensation were performed by Cytek Aurora Spectral Flow Cytometry.
other:Article Title: Human primary antibody response to vaccination follows a partially sequential class-switching program with a checkpoint at IGHG2.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER HRP-conjugated anti-human IgA (polyclonal) Sigma-Aldrich/Merk Cat# A0295-1ML; RRID: AB_257876 HRP-conjugated anti-human IgG (polyclonal) ThermoFisher Cat# A18817; RRID: AB_2535594 Biotin-conjugated goat anti-human IgG (polyclonal) Sigma-Aldrich/Merk Cat# AP112B; RRID: RRID:AB_92429 Biological samples PBMCs This study N/A Serum This study N/A Saliva This study N/A Saliva from SARS-CoV-2 infected individuals Stewart, Sinclair, Ng et al.8 N/A Chemicals, peptides, and recombinant proteins Streptavidin-BV421 1 (S1) Biolegend Cat# 405225 Streptavidin-APC 2 (S1) Biolegend Cat# 405207 Streptavidin-BUV737 (RBD) BD Biosciences Cat# 612775 Streptavidin-PE-Cy5 (Decoy, ex vivo B cell phenotyping) Biolegend Cat# 405205 Streptavidin-FITC (Decoy, sorting) Biolegend Cat# 405201 D-biotin SigmaAldrich Cat# B-4501 TotalSeqTM streptavidin-PE Biolegend Cat# 405261 TotalSeqTM streptavidin-APC Biolegend Cat# 405283 TotalSeqTM-C0971 Streptavidin Biolegend Cat# 405271 Biotin-S1 Biolegend Cat# 793806 Biotin-RBD Biolegend Cat# 793904 RBD for ELISA binding assay Abcam Cat# ab273065 S1 for ELISA binding assay R&D Systems Cat# 11058-CV FcR blocking agent Miltenyi Cat# 130-059-901 Critical commercial assays V-PLEX SARS-CoV-2 panel 30 (ACE2) Meso Scale Diagnostics (MSD) Cat# K15635U Chromium Next GEM Single cell 5′ reagent kit v2 (Dual Index) 10x Cat# PN-1000265 Deposited data Single-cell transcriptomics and BCR sequencing data generated in this manuscript This manuscript ArrayExpress: E-MTAB-16531 Bulk BCR repertoire data generated in this manuscript This manuscript https://doi.org/10.5281/zenodo.18187851 Whole blood flow cytometry data generated in this manuscript This manuscript https://fraternalilab.cs.ucl.ac.uk/ CovVaxBcells/ Antigen-specific B cell flow cytometry data generated in this manuscript This manuscript https://fraternalilab.cs.ucl.ac.uk/ CovVaxBcells/ Antibody titer measurement generated in this manuscript This manuscript https://fraternalilab.cs.ucl.ac.uk/ CovVaxBcells/ Peripheral blood B cell single-cell transcriptomics dataset from healthy individuals Stewart et al.16 ArrayExpress: E-MTAB-9544 Software and algorithms GraphPad Prism (v9) Domatics https://www.graphpad.com FlowJo (v10.8.1) BD Biosciences https://www.flowjo.com (Continued on next page) Cell Reports Medicine 7, 102848, July 21, 2026 e3 Article ll OPEN ACCESS
Suspension:Article Title: Apolipoprotein E drives microglia activation in the development of autoimmune uveitis through up-regulation of peptidyl prolyl isomerase F
Article Snippet: .. For surface receptor staining, the prepared cell suspension was treated with a mouse Fc receptor blocking agent (Miltenyi Biotec, 130-092-575, diluted 1:100) and incubated at 4°C for 20 min, followed by staining with specific antibodies at 4°C in the dark for 20 min. .. Cells were then fixed and permeabilized using a flow cytometry fixation/permeabilization buffer (Thermo Fisher Scientific, 00-5223-56 and 00-5123-43) at room temperature in the dark for 10 min. For intracellular cytokine staining, the cells were subsequently incubated with a flow cytometry permeabilization buffer (Thermo Fisher Scientific, 00-8333-56), followed by the addition of specific antibodies and incubation at room temperature in the dark for 20 min. Acquisition and compensation were performed by Cytek Aurora Spectral Flow Cytometry.
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