Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Antibodies | |||
| 7-AAD | Biolegend | Cat#420404 | |
| CD34-microbeads | Miltenyi | Cat#130-046-702 | |
| CD34-FITC | Miltenyi | Cat#130-113-178 | |
| CD49f-Pacific Blue | Biolegend | Cat#313620 | |
| CD90-PE | Biolegend | Cat#328110 | |
| CD38-PE/cy7 | Biolegend | Cat#303516 | |
| CD45RA-APC/cy7 | Biolegend | Cat#304128 | |
| CD20-Biotin | Biolegend | Cat#302350 | |
| CD56-Biotin | Biolegend | Cat#362536 | |
| CD14-Biotin | Biolegend | Cat#301826 | |
| Streptavidin-BV605 | BD | Cat#563260 | |
| CD14-APC | BD | Cat#340436 | |
| CD8-FITC | Biolegend | Cat#300906 | |
| CD14-microbeads | Miltenyi | Cat#130-050-201 | |
| Mouse lineage depletion kit | Miltenyi | Cat#130-090-858 | |
| FcX | Biolegend | Cat#156604 | |
| Ly6g-BUV395 | BD | Cat#563978 | |
| MHCII-BV421 | ThermoFisher | Cat#404-5321-82 | |
| CD11c-A488 | ThermoFisher | Cat#53-0114-82 | |
| CD86-PE | Biolegend | Cat#105105 | |
| CD206-BV605 | Biolegend | Cat#141721 | |
| CD4 PE-CF594 | BD | Cat#562285 | |
| CD19-APC | Thermofisher | Cat#17-0193-82 | |
| B220-APC | ThermoFisher | Cat#17-0452-82 | |
| CD45-A700 | Biolegend | Cat#103127 | |
| Ly6c-PerCP-Cy5.5 | Thermofisher | Cat#45-5932-82 | |
| CX3CR1-BV786 | Biolegend | Cat#149029 | |
| CD8-PE-Cy7 | Thermofisher | Cat#25-0081-82 | |
| CD11b-APC-e780 | ThermoFisher | Cat#47-0112-82 | |
| Aqua Live/Dead Viability dye | ThermoFisher | Cat#L34966 | |
| normal donkey serum | Jackson Immunoresearch | RRID: AB_2337258 | |
| Iba1 | Fujifilm | Cat#019-19741 | |
| GFAP | Cell Signaling Technologies | Cat#3657 | |
| MBP | Abcam | Cat#ab40390 | |
| anti-IgG secondary antibodies conjugated to A488 | Jackson Immunoresearch | RRID: AB_2338449 | |
| anti-IgG secondary antibodies conjugated to A594 | Jackson Immunoresearch | RRID: AB_2338873 | |
| anti-IgG secondary antibodies conjugated to A647 | Jackson Immunoresearch | RRID: AB_2338904 | |
| DAPI | Prolong Diamond Antifade | Cat#P36962 | |
| Bacterial and virus strains | |||
| MHV-1 | ATCC | VR-261 | |
| Biological samples | |||
| Paired PBMC and BMMC | AllCells | N/A | |
| Whole blood from study participants | Weill-Cornell Medicine/New York-Presbyterian Hospital | N/A | |
| Chemicals, peptides, and recombinant proteins | |||
| R848 | InvivoGen | Cat#tlrl-r848 | |
| mouse anti-IL-6R blocker | InVivoMab | Cat#BE0047 | |
| IFNα | PBL assay science | Cat#12100 | |
| RPMI medium | Corning | Cat#10-040-CM | |
| Ficoll-Paque PLUS | GE | Cat#17144002 | |
| Collagenase D | Roche | Cat#11088858001 | |
| Critical commercial assays | |||
| Chromium Controller & Next GEM Accessory Kit | 10x Genomics | Cat#1000202 | |
| Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle | 10x Genomics | Cat#1000285 | |
| NEBNext low input RNA library prep kit for Illumina | NEB | Cat#E6420S | |
| LEGENDplex Human anti-virus response panel (13-plex) | Biolegend | Cat#740390 | |
| 15-plex human pro-inflammatory cytokine assay | Eve Technologies | N/A | |
| TOP-Plus (Pylon 3D analyzer) for antibody level measurement | ET Healthcare | N/A | |
| Lung histology | HistoWiz | N/A | |
| Deposited data | |||
| Imaging mass cytometry | Rendeiro et al.70 | https://doi.org/10.5281/zenodo.4110560 | |
| GRCh38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/ | |
| GRCm38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/ | |
| Single-cell RNA-seq of human bone marrow | Granja et al.95 | GSE139369 | |
| ATAC-seq data of human HSPC subpopulation | Buenrostro et al.60 | GSE96772 | |
| Experimental models: Organisms/strains | |||
| A/J mouse | The Jackson Laboratory | Cat#000646 | |
| Software and algorithms | |||
| Cell Ranger ARC 1.0.0 | 10X Genomics | https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/latest | |
| Signac | Stuart et al.92 | https://stuartlab.org/signac/ | |
| Amulet | Thibodeau et al.93 | https://github.com/UcarLab/AMULET | |
| Seurat | Hao et al.94 | https://github.com/satijalab/seurat | |
| Scrublet | Wolock et al.95 | https://github.com/swolock/scrublet | |
| Harmony | Korsunsky et al.96 | https://github.com/immunogenomics/harmony | |
| MACS2 2.1.2 | Zhang et al.97 | https://github.com/macs3-project/MACS/wiki/Install-macs2 | |
| ArchR | Granja et al.98 | https://github.com/GreenleafLab/ArchR | |
| FigR | Kartha et al.99 | https://github.com/buenrostrolab/FigR | |
| Nebulosa | Alquicira-Hernandez et al.100 | https://github.com/powellgenomicslab/Nebulosa | |
| trimmomatic | Bolger et al.101 | https://github.com/timflutre/trimmomatic | |
| BWA | Li et al.102 | https://github.com/lh3/bwa | |
| Samtools | Li et al.103 | https://github.com/samtools | |
| Subread package | Liao et al.104 | https://subread.sourceforge.net/ | |
| IGV | James et al.105 | https://software.broadinstitute.org/software/igv/download | |
| snATACClusteringTools | Ucar Lab | https://github.com/UcarLab/snATACClusteringTools | |
| DiffBind | Stark et al.106 | https://hbctraining.github.io/Intro-to-ChIPseq/lessons/08_diffbind_differential_peaks.html | |
| ChipSeeker | Yu et al.107 | https://github.com/YuLab-SMU/ChIPseeker | |
| EdgeR | Robinson et al.108,109 | https://github.com/StoreyLab/edge | |
| cinaR | Karakaslar et al.110 | https://github.com/eonurk/cinaR | |
| HOMER 4.11 | Heinz et al.111 | http://homer.ucsd.edu/homer/ | |
| HINT | Gusmao et al.112 | https://github.com/CostaLab/reg-gen | |
| SparK | Kurtenbach et al.113 | https://github.com/harbourlab/SparK | |
| ClusterProfiler | Yu et al.114 | https://github.com/YuLab-SMU/clusterProfiler | |
| STAR 2.7.10b | Dobin et al.115 | https://github.com/alexdobin/STAR | |
| DESeq2 | Love et al.116 | https://git.bioconductor.org/packages/DESeq2 | |
| Snakemake | Mölder et al.117 | https://snakemake.readthedocs.io/en/stable/ | |
| Other | |||
| EDTA tubes | BD | Cat#366643 | |
| Heparin tubes | BD | Cat#368480 | |
| NovaSeq6000 | Illumina | N/A | |
| Zeiss LSM 900 | Carl Zeiss Microscopy | N/A | |
| Objective Plan-Apochromat 20x/0.8 M27 | Carl Zeiss Microscopy | N/A | |