REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
SARS-CoV-2 nucleocapsid	GeneTex	Cat#: GTX135361 RRID: AB_2887484
H1N1	Abcam	Cat#ab20343, RRID:AB_445525
CD68	Abcam	Cat# ab224029, clone:EPR20545
EpCAM	Abcam	Cat# ab213500, clone:EPR220532-222
alpha-SMA	Invitrogen	Cat# 53-9760-82, RRID:AB_2574461
KRT19	Thermofisher	Cat# TA803863, clone: OTI6A8
TGFBR2	Thermofisher	Cat# TA807912, clone: OTI3B4
F13A1	Abcam	Cat# ab225018, clone: EP3372
CD68	Santa Cruz	Cat# sc-20060 AF647, RRID:AB_627158
Biological samples
Patient paraffine embedded lung tissue	UAB Tissue Biorepository Core Facility	https://sites.uab.edu/tissuebank/
Chemicals, peptides, and recombinant proteins
Xylene	Fisher Scientific	Cat#X5P-1GAL
100% Ethanol	Fisher Scientific	Cat#HC-800-1GL
95% Ethanol	Fisher Scientific	Cat#HC-1100-1GL
Tris-EDTA ph9 buffer	Abcam	Cat#ab93684
Bovine Serum Albumin Fraction V	Fisher Scientific	Cat#BP1605-100
R-Phycoerythrin lightning-link labeling kit	Novus Biologicals	Cat#703-0010
Alexa 647 labeling kit	Thermofisher	Cat# A20186
PHEM buffer	Goldbio	https://www.goldbio.com/documents/3553/PHEM+Buffer+4X+Stock+Solution.pdf
DAPI	Biolegend	Cat#422801
ProLong Gold antifade mounting media	Thermofisher	Cat#P36934
Critical commercial assays
GeoMx Cancer Transcriptome Atlas (COVID-19)	Nanostring	https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-rna-assays/geomx-cancer-transcriptome-atlas/
Deposited data
Transcriptomics data	This paper	https://doi.org/10.17632/n5dn4xzg7j.1
Software and algorithms
Prism v7	GraphPad	https://www.graphpad.com/scientific-software/prism/
R v3.5.2	R project	https://www.r-project.org/
Microsoft Excel	Microsoft	https://www.microsoft.com/en-us/microsoft-365/p/excel/cfq7ttc0k7dx?activetab=pivot:overviewtab
Adobe Illustrator 2020	Adobe	https://www.adobe.com/products/illustrator.html
GSEA	Broad Insititute	https://www.gsea-msigdb.org/gsea/index.jsp
GeoMx DSP data center	Nanostring	https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-data-center/