Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-human CD19-PE, clone HIB19 | BioLegend | Cat. #302208; RRID: AB_314238 |
| Mouse anti-human CD23-PAC, clone EBVCS-5 | BioLegend | Cat. #338513; RRID: AB_1501123 |
| Mouse anti-human CD27-FITC, clone O323 | BioLegend | Cat. #302806; RRID: AB_314298 |
| Mouse anti-human CD27-APC, clone M-T271 | BioLegend | Cat. #356410; RRID: AB_2561957 |
| Mouse anti-human IgD-FITC, clone IA6-2 | BioLegend | Cat. #348206; RRID: AB_10612567 |
| Mouse anti-human CCR6-PE, clone R6H1 | Invitrogen | Cat. #12-1969-42; RRID: AB_1272087 |
| Bacterial and virus strains | ||
| Epstein-Barr Virus (EBV), B95-8 strain | Luftig Lab (original publication: Johannsen et al., 2004). | doi.org/10.1073/pnas.0407320101 |
| Biological samples | ||
| Whole blood samples, de-identified donors | Gulf Coast Regional Blood Center | N/A |
| Discarded tonsil tissue, anonymized | Duke University Medical Center | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| CellTrace Violet (proliferation tracking dye) | ThermoFisher / Invitrogen | Cat. #34571 |
| Histopaque-1077 density gradient medium | Sigma | Cat. #H8889 |
| Critical commercial assays | ||
| B cell Negative Isolation Kit | BD Biosciences | Cat. #558007 |
| Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns | 10x Genomics | Cat. #1000283 |
| Chromium Next GEM Chip J Single Cell, 16 rxns | 10x Genomics | Cat. #1000230 |
| Dual Index Kit TT Set A, 96 rxns | 10x Genomics | Cat. #1000215 |
| Chromium Next GEM Automated Single Cell 3’ Library and Gel bead Kit v3.1, 4 rxns | 10x Genomics | Cat. #1000147 |
| Chromium Next GEM Chip G Single Cell Kit, 16 rxns | 10x Genomics | Cat. #1000128 |
| Deposited data | ||
| Early infection scRNA + scATAC data (two biological donors, four timepoints per donor) | Luftig Lab | GSE189141; SRA #SRP346796 |
| Tonsil lymphocyte scRNA data | Luftig Lab | GSE159674; SRA #SRP287808 |
| Software and algorithms | ||
| cellranger-arc pipeline | 10x Genomics | v1.0.0 |
| cellranger pipeline | 10x Genomics | v3.0 & v2.0 |
| R | R Foundation | v4.0.5 |
| R Studio | RStudio, PBC | v1.4.1106 |
| Seurat | https://github.com/satijalab/seurat | v4.1 |
| SeuratWrappers | https://github.com/satijalab/seurat | v0.3.0 |
| Monocle3 | https://github.com/cole-trapnell-lab/monocle3/ | v1.0.0 |
| ggplot2 | Hadley Wickham | v3.3.6 |
| RColorBrewer | Erich Neuwirth | v1.1.3 |
| viridis | https://sjmgarnier.github.io/viridis/ | v0.6.2 |
| FlowJo | BD Biosciences | v10.8.1 |
| Cytoscape | Institute for Systems Biology | v3.9.1 |
| early_infection_analysis_code.R | Luftig Lab | DOI: 10.5281/zenodo.6821702 |