KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Vaccinia Virus (polycolonal) | Thermo Fisher Scientific | Cat#PA1-7258 |
| Anti-Rabbit IgG (H+L), HRP | Thermo Fisher Scientific | Cat#656120 |
| InVivoMAb anti-mouse CD8β (Clone 53-5.8) | BioXCell | Cat#BE0223 |
| InVivoMAb anti-mouse IFNAR-1 (Clone MAR1-5A3) | BioXCell | Cat#BE0241 |
| InVivoMAb Rat IgG1 (Clone HRPN) | BioXCell | Cat#BE0088 |
| InVivoMAb Mouse IgG1 Isotype control | BioXCell | Cat#BE0083 |
| TruStain fcX (anti-mouse CD16/32) (Clone 93) | Biolegend | Cat#101320 |
| Anti-mouse CCL5 PE (Clone 2E9/CCL5) | Biolegend | Cat#149103 |
| Anti-mouse CCR2 APC (Clone 475301) | R&D Systems | Cat#FAB5538A |
| Anti-mouse CD103 Brilliant Violet 510 (Clone 2E7) | Biolegend | Cat#121423 |
| Anti-mouse CD11b Alexa Fluor 700 (Clone M1/70) | Biolegend | Cat#101222 |
| Anti-mouse CD11b Brilliant Violet 421 (Clone M1/70) | Biolegend | Cat#101251 |
| Anti-mouse CD11c APC (Clone N418) | Biolegend | Cat#117310 |
| Anti-mouse CD11c PE/Cy7 (Clone N418) | Biolegend | Cat#117317 |
| Anti-mouse CD19 APC/Cy7 (Clone 6D5) | Biolegend | Cat#115529 |
| Anti-mouse CD19 FITC (Clone 6D5) | Biolegend | Cat#115506 |
| Anti-mouse CD24 PE/Cy7 (Clone M1/69) | Biolegend | Cat#101822 |
| Anti-mouse CD3ε APC (Clone 145-2C11) | Biolegend | Cat#100312 |
| Anti-mouse CD3ε APC/Cy7 (Clone 145-2C11) | Biolegend | Cat#100330 |
| Anti-mouse CD3ε FITC (Clone 145-2C11) | Biolegend | Cat#100306 |
| Anti-mouse CD44 PE/Cy7 (Clone IM7) | Biolegend | Cat#103030 |
| Anti-mouse CD45 Alexa Fluor 700 (Clone 30-F11) | Biolegend | Cat#103128 |
| Anti-mouse CD45 Brilliant Violet 510 (Clone 30-F11) | Biolegend | Cat#103137 |
| Anti-mouse CD45 PE (Clone 30-F11) | Biolegend | Cat#103106 |
| Anti-mouse CD45 PerCP/Cy5.5 (Clone 30-F11) | Biolegend | Cat#103132 |
| Anti-mouse CD45.1 PE (Clone A20) | Biolegend | Cat#110708 |
| Anti-mouse CD45.2 PerCP/Cy5.5 (Clone 104) | Biolegend | Cat#109828 |
| Anti-mouse CD49a PE (Clone HMα1) | Biolegend | Cat#142603 |
| Anti-mouse CD49b FITC (Clone DX5) | Biolegend | Cat#108905 |
| Anti-mouse CD62L APC (Clone MEL-14) | Biolegend | Cat#104412 |
| Anti-mouse CD64 PE (Clone X54-5/7.1) | Biolegend | Cat#139303 |
| Anti-mouse CD69 PE (Clone H1.2F3) | Biolegend | Cat#104508 |
| Anti-mouse CD8α Alexa Fluor 488 (Clone 53-6.7) | Biolegend | Cat#100723 |
| Anti-mouse CD8α PerCP (Clone 53-6.7) | Biolegend | Cat#100731 |
| Anti-mouse CD8β.2 FITC (Clone 53-5.8) | Biolegend | Cat#140403 |
| Anti-mouse CX3CR1 PE (Clone SA011F11) | Biolegend | Cat#149005 |
| Anti-mouse CXCR6 PE (Clone SA051D1) | Biolegend | Cat#151103 |
| Anti-mouse I-A/I-E Brilliant Violet 510 (Clone M5/114.15.2) | Biolegend | Cat#107635 |
| Anti-mouse I-A/I-E PE/Cy7 (Clone M5/114.15.2) | Biolegend | Cat#107630 |
| Anti-mouse IFN-γ FITC (Clone XMG1.2) | Biolegend | Cat#505806 |
| Anti-mouse/human KLRG1 PE (Clone 2F1/KLRG1) | Biolegend | Cat#138407 |
| Anti-mouse Ly6C APC/Cy7 (Clone HK1.4) | Biolegend | Cat#128026 |
| Anti-mouse Ly6C PE (Clone HK1.4) | Biolegend | Cat#128007 |
| Anti-mouse Ly6G FITC (Clone 1A8) | Biolegend | Cat#127606 |
| Antimouse I-A/I-E purified (Clone M5/114.15.2) | Biolegend | Cat#107602 |
| Anti-GFP (Clone GFP-G1) | DSHB | Cat#GFP-G1 |
| Anti-rat IgG (H+L) Alexa Fluor 555 | Thermo Fisher Scientific | Cat#A21434 |
| Anti-mouse IgG (H+L) Alexa Fluor 647 | Thermo Fisher Scientific | Cat#A31571 |
| Bacterial and Virus Strains | ||
| Vaccinia virus strain Western Reserve | BEI Resources | NR-55, Lot 3579605 |
| Vaccinia virus strain Western Reserve expressing eGFP | BEI Resources | NR-624, Lot 3925477 |
| Vaccinia virus strain Modified Vaccinia Ankara | BEI Resources | NR-726, Lot 4225252 |
| Vaccinia virus strain Modified Vaccinia Ankara expressing GFP | Bernard Verrier | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| H-2Kb VACV B8R20–27 (TSYKFESV) tetramer | NIH Tetramer Core Facility | N/A |
| SIGMAFAST OPD (o-Phenylenediamine dihydrochloride) | Sigma-Aldrich | Cat#P9187 |
| Gram Crystal Violet | BD | Cat#212525 |
| FTY720 | Sigma-Aldrich | Cat#SML0700; CAS: 162359-56-0 |
| Lymphocyte Separation Medium | Corning | Cat#25-072 |
| DNase I | Sigma-Aldrich | Cat#D4527 |
| Collagenase, Type IV | Worthington Biochemical Corporation | Cat#LS004188 |
| Liberase TL | Sigma-Aldrich | Cat#5401020001 |
| Percoll PLUS | GE Healthcare Life Sciences | Cat#17-5445-02 |
| RNAlater | Sigma-Aldrich | Cat#R0901 |
| VA-044 | Wako Pure Chemical Industries | Cat#VA-044; CAS: 27776-21-2 |
| Histodenz | Sigma-Aldrich | Cat#D2158; CAS: 66108-95-0 |
| Electrophoretic Tissue Clearing Solution | Logos Biosystems | Cat#C13001 |
| Zamboni Fixative | Newcomer Supply | Cat#1459A |
| Benzyl alcohol | Sigma-Aldrich | Cat#402834; CAS: 100-51-6 |
| Benzyl benzoate | Sigma-Aldrich | Cat#B6630; CAS: 120-51-4 |
| RNase Block Ribonuclease Inhibitor | Agilent Technologies | Cat#300151 |
| Klenow Fragment (3’->5’ exo-) | New England Biolabs | Cat#M0212 |
| TURBO DNase | Thermo Fisher Scientific | Cat#AM2239 |
| Exonuclease I | New England Biolabs | Cat#M0293 |
| Critical Commercial Assays | ||
| BD Cytofix/Cytoperm Fixation/Permeabilization Kit | BD | Cat#554714 |
| High-Capacity cDNA Reverese Transcription Kit | Thermo Fisher Scientific | Cat#4368813 |
| LightCycler 480 SYBR Green I Master | Roche | Cat#04887352001 |
| Stainless Steel Bead, 5 mm | QIAGEN | Cat#69989 |
| Isol-RNA Lysis Reagent | 5Prime | Cat#2302700 |
| Dynabeads MyOne Silane | Thermo Fisher Scientific | Cat#37002D |
| Buffer RLT | QIAGEN | Cat#79216 |
| Quanti-iT RiboGreen RNA Assay Kit | Thermo Fisher Scientific | Cat#R11490 |
| AffinityScript Multiple Temperature Reverse Transcriptase | Agilent Technologies | Cat#600109 |
| RNA Clean & Concentrator-5 | Zymo Research | Cat#R1015 |
| Oligo Clean & Concentrator | Zymo Research | Cat#D4060 |
| Agencourt AMPure XP | Beckman Coulter | Cat#A63880 |
| Q5 Hot Start High-Fidelity 2X Master Mix | New England Biolabs | Cat#M0494 |
| E-Gel EX Agarose Gels, 2% | Thermo Fisher Scientific | Cat#G402002 |
| Qubit dsDNA High Sensitivity Assay Kit | Thermo Fisher Scientific | Cat#Q32854 |
| RiboLock RNase Inhibitor | Thermo Fisher Scientific | Cat#EO0381 |
| Maxima H Minus Reverse Transcriptase | Thermo Fisher Scientific | Cat#EP0753 |
| DNA Clean & Concentrator-5 | Zymo Research | Cat#D4013 |
| Advantage 2 PCR Kit | Clontech | Cat#639206 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat#FC-131-1024 |
| Deposited Data | ||
| Whole-tissue and bulk sort RNA-seq data sets | This paper | GEO: GSE87633 |
| Single-cell RNA-seq data sets | This paper | GEO: GSE90697 |
| Experimental Models: Cell Lines | ||
| African green monkey: Vero | ATCC | Cat#CCL-81 |
| Syrian golden hamster: BHK-21 | ATCC | Cat#CCL-10 |
| Human: Hela S3 | ATCC | Cat#CCL-2.2 |
| African green monkey: BS-C-1 | ATCC | Cat#CCL-26 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | JAX | stock 000664 |
| Mouse: Csf2−/− (B6.129S-Csf2tm1Mlg/J) | JAX | stock 026812 |
| Mouse: Ifng−/− (B6.129S7-Ifngtm1Ts/J) | JAX | stock 002287 |
| Mouse: Il22−/− (C57BL/6-Il22tm1.1(icre)Stck/J) | JAX | stock 027524 |
| Mouse: Ifnar1−/− | Christophe Benoist, Diane Mathis and Mei X. Wu | N/A |
| Mouse: Tcra−/− | Arlene Sharpe | N/A |
| Oligonucleotides | ||
| Primers for qPCR, custom RNA-seq and single-cell RNA-seq, see Table S7 | This paper | N/A |
| Software and Algorithms | ||
| R version 3.3.2 | The R Project | https://www.r-project.org |
| RStudio Version 1.0.136 | N/A | https://www.rstudio.com |
| CFX Manager | Bio-Rad | http://www.bio-rad.com/en-us/product/cfx-manager-software |
| Fiji version 2.0.0 | NIH | https://fiji.sc |
| ZEN microscope software | ZEISS | https://www.zeiss.com/microscopy/us/products/microscope-software/zen/image-analysis.html |
| MAFFT | Katoh and Standley, 2013 | http://mafft.cbrc.jp/alignment/software/ |
| Circos | Krzywinski et al., 2009 | http://circos.ca/ |
| STAR version 2.5.2b | Dobin et al., 2013 | https://code.google.com/archive/p/rna-star/ |
| FastQC | N/A | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Qualimap | Garcia-Alcalde et al., 2012 | http://qualimap.bioinfo.cipf.es/ |
| MultiQC | N/A | https://github.com/ewels/MultiQC |
| featureCounts version 1.4.4 | Liao et al., 2014 | http://bioinf.wehi.edu.au/featureCounts/ |
| Sailfish version 0.9.2 | Patro et al., 2014 | https://www.cs.cmu.edu/~ckingsf/software/sailfish/ |
| Limma | Ritchie et al., 2015 | http://bioinf.wehi.edu.au/limma/ |
| DAVID | Huang et al., 2009 | https://david.ncifcrf.gov/ |
| GENE-E | The Broad Institute | https://software.broadinstitute.org/GENE-E/ |