KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-CD19 APC Cy7, Clone 1D3 | BD Biosciences | Cat# 557655, RRID:AB_396770 |
| Anti-CD45.1 APC, Clone A20 | BD Biosciences | Cat# 558701, RRID:AB_1645214 |
| Anti-CD45.1 APC R700, Clone A20 | BD Biosciences | Cat# 565813, RRID:AB_2744397 |
| Anti-CD45.1 BV510, Clone A20 | BD Biosciences | Cat# 565278, RRID:AB_2739150 |
| Anti-CD45.1 PECy7, Clone A20 | BD Biosciences | Cat# 560578, RRID:AB_1727488 |
| Anti-CD45.2 PECy7, Clone 104 | BD Biosciences | Cat# 560696, RRID:AB_1727494 |
| Anti-CD45.2 PE, Clone 104 | BD Biosciences | Cat# 560695, RRID:AB_1727493 |
| Anti-CD45.2 BV711, Clone 104 | BD Biosciences | Cat# 563685, RRID:AB_2738374 |
| Anti-Bcl6 PE, Clone K112-91 | BD Biosciences | Cat# 561522, RRID:AB_10717126 |
| Anti-CD138 BV510, Clone 281-2 | BD Biosciences | Cat# 558626, RRID:AB_1645216 |
| Anti-CD38 APC, Clone 90/CD38 | BD Biosciences | Cat# 102711, RRID:AB_312932 |
| Anti-CD4 BV711, Clone RM4-5 | BD Biosciences | Cat# 563726, RRID:AB_2738389 |
| Anti-CD4 PE, Clone RM4-5 | BD Biosciences | Cat# 553049, RRID:AB_394585 |
| Anti-CD95 BV421, Clone Jo2 | BD Biosciences | Cat# 562633, RRID:AB_2737690 |
| Anti-CD95 FITC, Clone Jo2 | BD Biosciences | Cat# 554257, RRID:AB_395329 |
| Anti-CD95 APC R700, Clone Jo2 | BD Biosciences | Cat# 565130, RRID:AB_2739078 |
| Anti-CXCR3 BV421, Clone CXCR3-173 | BioLegend | Cat# 126522, RRID:AB_2562205 |
| Anti-CXCR3 PECy7, Clone CXCR3-173 | BioLegend | Cat# 126516, RRID:AB_2245493 |
| Anti-CXCR5 Biotin, Clone 2G8 | BD Biosciences | Cat# 551960, RRID:AB_394301 |
| Anti-CXCR5 Biotin, Clone SPRCL5 | eBioscience | Cat# 13-7185-82, RRID:AB_2572800 |
| Anti-IgD FITC, Clone 11-26c.2a | BD Biosciences | Cat# 562022, RRID:AB_10894208 |
| Anti-IgM PECy7, Clone ll / 41 | eBioscience | Cat# 25-5790-82, RRID:AB_469655 |
| Anti-IFNγ PECy7, Clone XMG1.2 | BD Biosciences | Cat# 557649, RRID:AB_396766 |
| Anti-PD1 FITC, Clone J43 | eBioscience | Cat# 11-9985-85, RRID:AB_465473 |
| Anti-PD1 eFluorTM 450, Clone J43 | eBioscience | Cat# 48-9985-82, RRID:AB_2574139 |
| Anti-T-bet PECy7, Clone 4B10 | BioLegend | Cat# 644823, RRID:AB_2561760 |
| Anti-T-bet APC, Clone 4B10 | BioLegend | Cat# 644814, RRID:AB_10901173 |
| Anti-CD184 (CXCR4) PE, Clone 2B11 | BD Biosciences | 551966, RRID:AB_394305 |
| Anti-CD196 (CCR6) Alexa Fluor 647, Clone140706 | BD Biosciences | 557976, RRID:AB_2228793 |
| Anti-CD196 (CCR6) BV510, Clone140706 | BD Biosciences | Cat# 747832, RRID:AB_2872295 |
| anti-CD154, Clone MR-1 | BioXCell | Cat# BE0017-1, RRID:AB_1107601 |
| Streptavidin, V500 | BD Biosciences | Cat# 561419, RRID:AB_10611863 |
| HRP-conjugated goat Anti-Mouse IgG | Southern Biotech | Cat# 1030-05, RRID:AB_2619742 |
| HRP-conjugated Goat Anti-Mouse IgG2c | Southern Biotech | 1079-05, RRID:AB_2794466 |
| Bacterial and Virus Strains | ||
| PR8-OTII | Lee et al., 200551 | N/A |
| X31 | Lee et al., 200551 | N/A |
| A/PR8/34 (PR8) | Thomas et al., 201652 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| PMA | Sigma-Aldrich | Cat# P8139-1MG |
| Calcimycin | Life Technologies | Cat# A1493 |
| Brefeldin-A | Sigma-Aldrich | Cat# B7651-5MG |
| DNAse I | Qiagen | Cat# 79254 |
| 7-AAD | Calbiochem | Cat# 12-993-51 |
| Recombinant NP tetramer | Allie et al., 2019 1 | N/A |
| Alkaline phosphatase substrate BCIP/NBT | Moss Substrates | Cat#NBIM-1000 |
| Critical Commercial Assays | ||
| EasySep™ CD4+ positive selection kit | STEMCELL Technologies | Cat# 18952 |
| BD Cytofix/Cytoperm™ Fixation and Permeabilization Solution | BD Biosciences | Cat# 554722 |
| Norgen Single Cell RNA Purification Kit | Norgen Biotek | Cat# 51800 |
| Transcription factor staining buffer set | eBioscience | Cat# 00-5523-00 |
| Deposited Data | ||
| RNA-seq data | This paper | GSE208322. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208322 |
| Public pre-MEM signature | Laidlaw et al., 2017 18 | GSE89897 |
| Public pre-MEM signature | Wang et al., 2017 21 | GSE85018. |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6 (B6) | The Jackson Laboratories | Strain #:000664 RRID:IMSR_JAX:000664 |
| Mouse: B6.SJL-Ptprca Pepcb/BoyJ | The Jackson Laboratories | Strain #:002014 RRID:IMSR_JAX:002014 |
| Mouse: B6.129P2-Tcrβtm1MomTcrδtm1Mom | The Jackson Laboratories | N/A |
| Mouse: C57BL/6-Tg(TcraTcrb)425Cbn/J | The Jackson Laboratories | Strain #:004194 RRID:IMSR_JAX:004194 |
| Mouse: B6.129S6-Tbx21tm1Glm/J | The Jackson Laboratories | Strain #:004648 RRID:IMSR_JAX:004648 |
| Mouse: B6.129S7-Ifngr1tm1Agt/J | The Jackson Laboratories | Strain #:003288 RRID:IMSR_JAX:003288 |
| Mouse: B6.129P2-Cxcr3tm1Dgen/J | The Jackson Laboratories | Strain #:005796 RRID:IMSR_JAX:005796 |
| Mouse: B6.129S7-Ifngtm1Ts/J | The Jackson Laboratories | Strain #:002287 RRID:IMSR_JAX:002287 |
| Mouse: B6.129S(Cg)-Stat1tm1Dlv/J | The Jackson Laboratories | Strain #:012606 RRID:IMSR_JAX:012606 |
| Mouse: Tg(Cd4-cre)1Cwi/BfluJ | The Jackson Laboratories | Strain #:017336 RRID:IMSR_JAX:017336 |
| Mouse: B6.Bcl6fl/fl | Laboratory of Dr. Changchun Xiao (Scripps Research Institute) 50 | N/A |
| Mouse: B6.129-Il4tm1Lky/J (B6.4get IL-4 reporter mice) | Laboratory of Dr. M. Mohrs (Trudeau Institute) | N/A |
| Software and Algorithms | ||
| Prism V9 | GraphPad | https://www.graphpad.com/ |
| FlowJo V10.8.0 | TreeStar | https://www.flowjo.com |
| javaGSEA V3.0 | Broad Institute | http://www.gsea-msigdb.org/gsea/index.jsp |
| MATLAB | The Mathworks Inc. | https://www.mathworks.com/products/matlab/whatsnew.html |
| fastQC | Babraham Bioinformatics | http://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| Trim Galore V0.4.4. | Babraham Bioinformatics | http://www.bioinformatics.babraham.ac.uk/projects/trim_galore |
| STAR aligner V2.5.2a | Ilumina | https://support.illumina.com/sequencing/sequencing_software/igenome.html |
| Ingenuity Pathway Analysis | Qiagen | https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/ |
| R package edgeR | Robinson et al., 2019 56 | https://www.bioconductor.org |