Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | Anti-CD41a (mouse monoclonal) | eBioscience | Cat#17-0411-82 RRID:AB_1603237 |
FACS (1 μl per test) |
| Antibody | Anti-CXCR4 (mouse monoclonal) | eBioscience | Cat#53-9991-80 RRID:AB_953573 | FACS (1 μl per test) |
| Antibody | Anti-CD11b (mouse monoclonal) | eBioscience | Cat#12-0112-82 RRID:AB_2734869 | FACS (1 μl per test) |
| Antibody | Anti-F4/80 (mouse monoclonal) | eBioscience | Cat#17-4801-80 RRID:AB_2784647 | FACS (1 μl per test) |
| Antibody | Anti-Gr-1 (mouse monoclonal) | Biolegend | Cat#108424 RRID:AB_2137485 | FACS (1 μl per test) |
| Antibody | Anti-Ly-6C (mouse monoclonal) | Biolegend | Cat#128022 RRID:AB_10639728 | FACS (1 μl per test) |
| Antibody | Anti-CD11c (mouse monoclonal) | eBioscience | Cat#12-0114-82 RRID:AB_465552 | FACS (1 μl per test) |
| Antibody | Anti-CD45.1 (mouse monoclonal) | eBioscience | Cat#15-0453-82 RRID:AB_468759 | FACS (1 μl per test) |
| Antibody | Anti-CD45.2 (mouse monoclonal) | Biolegend | Cat#109831 RRID:AB_10900256 | FACS (1 μl per test) |
| Antibody | Anti-CD4 (mouse monoclonal) | eBioscience | Cat#12-0041-82 RRID:AB_465506 | FACS (1 μl per test) |
| Antibody | Anti-CD8a (mouse monoclonal) | Biolegend | Cat#100707 RRID:AB_312746 | FACS (1 μl per test) |
| Antibody | Anti-IFN-γ (mouse monoclonal) | Biolegend | Cat#505813 RRID:AB_493312 | FACS (1 μl per test) |
| Antibody | Anti-IL-4 (mouse monoclonal) | Biolegend | Cat#504118 RRID:AB_10898116 | FACS (1 μl per test) |
| Antibody | Anti-CD34 (mouse monoclonal) | eBioscience | Cat#11-0341-82 RRID:AB_465021 | FACS (1 μl per test) |
| Antibody | Anti-Sca-1 (mouse monoclonal) | Biolegend | Cat#108114 RRID:AB_493596 | FACS (1 μl per test) |
| Antibody | Anti-c-Kit (mouse monoclonal) | Biolegend | Cat#105812 RRID:AB_313221 | FACS (1 μl per test) |
| Antibody | Anti-CD135 (mouse monoclonal) | Biolegend | Cat#135314 RRID:AB_2562339 | FACS (1 μl per test) |
| Antibody | Anti-CD3ε (mouse monoclonal) | Biolegend | Cat#100310 RRID:AB_312675 | FACS (1 μl per test) |
| Antibody | Anti-B220 (mouse monoclonal) | Biolegend | Cat#103210 RRID:AB_312995 | FACS (1 μl per test) |
| Antibody | Anti-TER-119 (mouse monoclonal) | Biolegend | Cat#116210 RRID:AB_313711 | FACS (1 μl per test) |
| Antibody | Anti-IgM (mouse monoclonal) | eBioscience | Cat#15-5790-82 RRID:AB_494222 | FACS (1 μl per test) |
| Antibody | Anti-CD16/32 (mouse monoclonal) | Biolegend | Cat#101333 RRID:AB_2563692 | FACS (1 μl per test) |
| Antibody | Anti-CD127 (mouse monoclonal) | Biolegend | Cat#135021 RRID:AB_1937274 | FACS (1 μl per test) |
| Antibody | Anti-TNFα (mouse monoclonal) | Invitrogen | Cat#17-7321-81 RRID:AB_469507 | FACS (1 μl per test) IF (1:100) |
| Antibody | Anti-IL-6 (mouse monoclonal) | Biolegend | Cat#504507 RRID:AB_10694868 | FACS (1 μl per test) IF (1:100) |
| Antibody | Anti-BrdU (mouse monoclonal) | eBioscience | Cat#11-5071-42 RRID:AB_11042627 | FACS (1 μl per test) |
| Antibody | Anti-Endomucin (mouse polyclonal) | R&D | Cat#AF4666 | IF (1:100) |
| Antibody | Anti-CD150 (mouse monoclonal) | Biolegend | Cat#115908 RRID:AB_345278 | IF (1:100) |
| Antibody | Anti-Lineage Panel (mouse monoclonal) | Biolegend | Cat#133307 RRID:AB_11124348 | IF (1:100) |
| Antibody | Anti-Goat AF488 (goat polyclonal) | Invitrogen | Cat#A32814 RRID:AB_2762838 | IF (1:1000) |
| Antibody | Anti-TNF-alpha (mouse monoclonal) | Sino Biological | Cat#50349-R023 | 2 μg ml–1 |
| Antibody | Anti-Rabbit AF488 (rabbit polyclonal) | Invitrogen | Cat#R37118 RRID:AB_2556546 | IF (1:1000) |
| Antibody | Anti-OVA257-264 (SIINFEKL) peptide bound to H-2Kb (mouse monoclonal) | Invitrogen | Cat#17-5743-82 RRID:AB_1311286 | FACS (1 μl per test) |
| Antibody | Anti-IL-2 (mouse monoclonal) | eBioscience | Cat#25-7021-80 RRID:AB_1235007 | FACS (1 μl per test) |
| Chemical compound, drug | Diphtheria toxin (DT) | Sigma-Aldrich | Cat#D0564-1MG | 40 μg kg–1 body mass |
| Chemical compound, drug | BrdU (5-Bromo-2´-Deoxyuridine) | Sigma-Aldrich | Cat#B5002-250mg | 125 mg kg–1 body mass |
| Chemical compound, drug | CFSE (5-Carboxyfluorescein, Succinimidyl Ester) | Invitrogen | Cat#C2210 | 2.5 μM |
| Chemical compound, drug | GM-CSF | Abbkine | Cat#PRP2116 | 10 ng ml–1 |
| Chemical compound, drug | IL-4 | novoprotein | Cat#CK15 | 10 ng ml–1 |
| Chemical compound, drug | Tamoxifen | Sigma-Aldrich | Cat#T5648 | 20 mg ml–1 corn oil |
| Commercial kit | Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 | 10 x Genomics | PN-1000075 | |
| Commercial kit | Chromium Chip B Single Cell Kit | 10 x Genomics | PN-1000074 | |
| Cell line (Mus musculus) | NCTC clone 929 | ATCC | CCL-1 RRID:CVCL_0462 |
|
| Cell line (Mus musculus) | B3Z hybridoma CD8 T cell | Dr. Nilabh Shastri | ||
| Other | scRNA sequencing data (raw and processed data) | This paper | GEO: GSE168224 | |
| Genetic reagent (Mus musculus) | C57BL/6 J | Shanghai Model Organisms | ||
| Genetic reagent (Mus musculus) | Tg(Pf4-icre)Q3Rsko/J (Pf4Cre) | Jackson Laboratory | Stock No: 008535 | |
| Genetic reagent (Mus musculus) | Gt(ROSA) 26Sortm1(HBEGF) Awai/J (Rosa26fs-iDTR) | Jackson Laboratory | Stock No: 007900 | |
| Genetic reagent (Mus musculus) | Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J (Rosa26fs-mTmG) | Jackson Laboratory | Stock No: 007576 | |
| Genetic reagent (Mus musculus) | Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J (Rosa26fs-tdTomato) | Jackson Laboratory | Stock No: 007905 | |
| Genetic reagent (Mus musculus) | SclCreER mice | Göthert et al., 2005 | ||
| Genetic reagent (Mus musculus) | Cxcl12tm2.1Sjm/J (Cxcl12fs-DsRed) | Jackson Laboratory | Stock No: 022458 | |
| Genetic reagent (Mus musculus) | C57BL/6-Tg(TcraTcrb)1,100Mjb/J (OT-I) | Jackson Laboratory | Stock No: 003831 | |
| Strain, strain background (L. monocytogenes) | 10403 S | Bishop and Hinrichs, 1987 | ||
| Software, algorithm | Cell ranger_3.0.2 | 10 x Genomics | tenx RRID:SCR_01695 |
|
| Software, algorithm | R_3.6.3 | https://cran.r-project.org/ | R 3.6.3 | |
| Software, algorithm | Seurat_3.0.2 | Butler et al., 2018 | Seurat RRID:SCR_016341 |
|
| Software, algorithm | ggplot2_3.2.0 | https://cran.r-project.org/web/packages/ggplot2/index.html | ggplot2 RRID:SCR_014601 | |
| Software, algorithm | clusterProfiler_3.12.0 | Yu et al., 2012 | clusterProfiler RRID:SCR_016884 | |
| Software, algorithm | pheatmap_1.0.12 | https://cran.r-project.org/web/packages/pheatmap/ | pheatmap RRID:SCR_016418 | |
| Software, algorithm | CellPhoneDB_2.1.7 | Efremova et al., 2020 | CellPhoneDB RRID:SCR_017054 | |
| Software, algorithm | CellChat_1.1.3 | Jin et al., 2021 | CellChat 1.1.3 | |
| Software, algorithm | symphony_1.0 | Kang et al., 2021 | symphony 1.0 | |
| Software, algorithm | MetaNeighbor_1.10.0 | Crow et al., 2018 | MetaNeighbor RRID:SCR_016727 | |
| Software, algorithm | iMAP_1.0.0 |
Wang et al., 2021b
|
iMAP 1.0.0 | |
| Software, algorithm | scmap_ 1.16.0 | Kiselev et al., 2018 | Scmap RRID:SCR_017338 | |
| Software, algorithm | enrichplot_1.4.0 | Yu, 2019 | enrichplot 1.4.0 | |
| Software, algorithm | Imaris_8.4 | Bitplane | Imaris RRID:SCR_007370 | |
| Software, algorithm | FlowJo_10 | BD Bioscience | FlowJo RRID:SCR_008520 | |
| Software, algorithm | ImageJ_ 1.8.0 | National Institutes of Health | ImageJ RRID:SCR_003070 | |
| Other | DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride) | Thermo Fisher | Cat#D1306 | IF (0.5 µg/mL) |
| Other | Corn oil | Sigma-Aldrich | Cat#PHR2897 | Tamoxifen dissolution |
| Other | Lymphocyte Separation Medium | TBD Science | Cat#LTS1077 | Liver cell isolation |