REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-SARS-CoV-2 nucleocapsid	GeneTex	Cat#GTX135357; RRID AB_2868464
Rabbit anti-IBA1	Wako Chemicals	Cat#019-19741; RRID: AB_839504
Rat anti-CD68	Abcam	Cat#ab53444; RRID: AB_869007
Rabbit anti-DCX	Abcam	Cat#ab18723; RRID: AB_732011
Rabbit anti-ASPA	EMD Millipore	Cat#ABN1698; RRID: AB_2827931
Goat anti-PDGFRa	R&D Systems	Cat#AF1062; RRID: AB_2236897
Mouse anti-CC1	EMD Millipore	Cat#OP80; RRID: AB_2057371
Chicken anti-NeuN	EMD Millipore	Cat#ABN91; RRID: AB_11205760
Alexa 647 donkey anti-rabbit IgG	Jackson Immunoresearch	Cat# 711-605-152; RRID: AB_2492288
Alexa 488 donkey anti rat IgG	Jackson Immunoresearch	Cat# 712-545-153; RRID: AB_2340684
Alexa 594 donkey anti-rabbit IgG	Jackson Immunoresearch	Cat# 711-585-152; RRID: AB_2340621
Alexa 488 donkey anti goat IgG	Jackson Immunoresearch	Cat# 705-545-147; RRID: AB_2336933
Alexa 647 donkey anti-mouse IgG	Jackson Immunoresearch	Cat# 715-605-150; RRID: AB_2340862
DAPI	Thermo Fisher Scientific	Cat# 62247
Prolong Gold Mounting Medium	Life Technologies	Cat# P36930
Normal Donkey Serum	Jackson Immunotherapy	Cat# 017-000-121
Mouse anti-CD68	Thermo Fisher Scientific	Cat# 14-0688-82; RRID: AB_11151139
PowerVision polyHRP anti-mouse IgG	Leica Biosystems	Cat# PV6114; RRID: AB_1307589
PowerVision polyHRP anti-rabbit IgG	Leica Biosystems	Cat# PV6119; RRID: AB_1307590
Bacterial and virus strains
AAV-CMV-hACE2	Janelia Viral tools	N/A
Biological samples
SARS-Related Coronavirus 2, Isolate USA-WA1/2020	BEI resources	Cat# NR-52281
Chemicals, peptides, and recombinant proteins
8% Glutaraldehyde	Electron Microscopy Services	Cat#16000
16% Paraformaldehyde	Electron Microscopy Services	Cat#15700
0.1 M sodium cacodylate	Electron Microscopy Services	Cat#12300
3,3′- diaminobenzidine (DAB)	Vector Laboratories	Cat# SK-4100
Hematoxylin Solution	DAKO	Cat# CS70030-2
EcoMount Mounting Medium	Biocare Medical	Cat# EM897L
Critical commercial assays
Immune Monitoring 48-Plex Mouse ProcartaPlex Panel	Thermo Fisher Scientific	Cat# EPX480-20834-901
Human Cytokine/Chemokine 71-Plex Discovery Assay Array	Eve Technologies	Cat# HD71
Recombinant Mouse CCL11/Eotaxin protein	R&D Systems	Cat# 420-ME-020/CF
Deposited data
Single Cell sequencing dataset	NCBI Sequencing Read Archive (SRA) BioProject	NCBI: PRJNA833593
Experimental models: Organisms/strains
Mouse: CD1	Charles River	Strain #022
Mouse: Balb/cJ	Jackson Laboratory	Strain #000651
Software and algorithms
FIJI	NIH	https://imagej.net/software/fiji/
Zen	Zeiss	https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html
Imaris image analysis software	Oxford Instruments	https://imaris.oxinst.com/packages
Graphpad Prism	Dotmatics	https://www.graphpad.com/
R (v4.1.1)	R Core Team	https://www.r-project.org/
Suerat (v4.1.0)	Hao et al. (2021)	https://github.com/satijalab/seurat
Harmony (v0.1.0)	Korsunsky et al. (2019)	https://github.com/immunogenomics/harmony
Speckle (v0.0.3)	Phipson et al. (2021)	https://doi.org/10.1101/2021.11.28.470236
clusterProfiler package (v4.0.5)	Wu et al. (2021)	N/A
simplifyEnrichment package (v1.2.0)	Gu and Hübschmann (2021)	https://doi.org/10.1101/2020.10.27.312116
UpsetR package (v1.4.0)	Conway et al. (2017)	https://github.com/hms-dbmi/UpSetR/