REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Alexa Fluor® 488 anti-mouse CD8a Antibody	Biolegend	Clone 53-6.7 Cat.# 100723; AB_389304
PerCP-Cyanine5.5 CD16/CD32 Monoclonal Antibody	eBioscience	Clone 93 Cat.# 45-0161-82; AB_996659
eFluor 450 CD4 Monoclonal Antibody	eBioscience	Clone RM4-5 Cat.# 48-0042-82; AB_1272194
PE TNF alpha Monoclonal Antibody	eBioscience	Clone MP6-XT22 Cat.# 12-7321-82; AB_466199
APC IFN gamma Monoclonal Antibody	eBioscience	Clone XMG1.2 Cat.# 17-7311-82; AB_469504
mouse anti-human hACE2 antibody	R&D Systems	Cat.# MAB933; AB_2223153
mouse anti-β-actin	Genscript	Cat.# A01546; AB_1968817
rabbit anti-SARS-CoV-2 nucleocapsid protein polyclonal antibody	Sino Biological	Cat.# 40143-T62
HRP-labeled goat anti-rabbit secondary antibody	Jackson ImmunoResearch Laboratories	Cat.# 111-035-144; AB_2307391
anti-CD4 antibody	Bio X Cell	Clone GK1.5 Cat.# BE0003-1; AB_1107636
anti-CD8 antibody	Bio X Cell	Clone 2.43 Cat.# BE0061; AB_1125541
Virus Strains
SARS-CoV-2/human/CHN/IQTC01/2020 (GenBank: MT123290.1)		N/A
2019-nCoV/USA-WA1/2020(GenBank: MN985325.1)		N/A
Chemicals and Peptides
Remdesivir	MedChemExpress	Cat.# HY-104077
Sulfobutylether-β-Cyclodextrin	MedChemExpress	Cat.# HY-17031
Poly I:C	Invivogen	Cat.# 31852-29-6
Agarose	RPI	Cat.# 9012-36-6
Crystal violet	Solarbio	Cat.# C8470
4% Paraformaldehyde	Biosharp	Cat.# BL539A
Zinc formalin	Sigma	Cat.# Z2902
Triton X-100	Solarbio	Cat.# T8200
GolgiPlug Protein Trnsp Inbb	BD Biosciences	Cat.# 555029
Cytofix/Cytoperm Solution	BD Biosciences	Cat.# 554722
Carboxymethylcellulose powder	Sigma	Cat.#C4888
TrueBlue™ Peroxidase Substrate (KPL, Gaithersburg, MD)	SeraCare	Cat.# 510-0030
Blocking reagent	Biocare Medical	Cat.# RBM961H
Secondary Kit (Mouse Envision)	Dako	Cat.# K00111-2
DAB+ Substrate Chromogen System (Dako Omnis)	Dako	Cat.# GV825
Streptavidin-horseradish peroxidase conjugate (Vectastain ABC Elite kit)	Vector Labs	Cat.# PK-8200
Diaminobenzidine	Vector Labs	Cat.# SK-4100
NovaRED	Vector Labs	Cat.# SK-4805
RNA ScreenTape	Agilent Technologies	Cat.# 5067-5576
RNA Reagent	Agilent Technologies	5067-5577
D1000 ScreenTape	Agilent Technologies	5067-5582
D1000 Reagent	Agilent Technologies	5067-5583
Qubit® dsDNA HS Assay Kit	Life Technologies	Q32851
QIAseq FastSelect –rRNA HMR Kits	QIAGEN	334387
NEBNext® UltraTM RNA Library Prep Kit for Illumina	NEB	E7530L
SuperSignal West Pico Trial Kit	Thermo Scientific	N/A
Trizol	invitrogen	Cat.# 15596018
Fetal Bovine Sera	GIBCO	Cat.# 10270-106
Penicillin-Streptomycin	Invitrogen	Cat.# 60106-1
L-GLUTAMINE,100X	Invitrogen	Cat.# 2503081
DPBS	GIBCO	Cat.# 14190235
RPMI1640	Life	Cat.# C11875500BT
DMEM	Life	Cat.# C11965500BT
Deposited Data
Raw and analyzed data	This paper	GEO: 150847
Experimental Models: Cell Lines
Vero E6 cells	ATCC	CRL-1586
Calu-3 cells	ATCC	HTB-55
17Cl-1 cells	ATCC
Experimental Models: Organisms/Strains
Mouse: WT C57BL/6 mouse	Hunan SJA Laboratory Animal Co.(China) Charles River Laboratories (USA)	N/A
Mouse: WT BALB/c mouse	Hunan SJA Laboratory Animal Co.(China) Charles River Laboratories (USA)	N/A
Mouse: IFNARKO C57BL/6 mouse	Jackson Laboratories	JAX: 028288
Mouse: B6.129S(Cg)-Stat1tm1Dlv/J	Jackson Laboratories	JAX: 012606
Mouse: B6.129S7-Ifng tm1Ts J	Jackson Laboratories	JAX: 002287
Software and Algorithms
FlowJo VX		N/A
GraphPad Prism V7.04		N/A
Bowtie2 v2.2.5	Langmead and Salzberg, 2012	N/A
RSEM v1.2.22	Li and Dewey, 2011	N/A
EDASEQ v2.16	Risso et al., 2011	N/A
DESeq2 v1.22.1	Love et al., 2014	N/A
clusterProfiler v3.10.0	Hutchins et al., 2014	N/A