REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Actin (Pan)	Thermo Fisher Scientific	Cat# MS-1295, RRID:AB_63314
Rabbit monoclonal anti-GAPDH, Clone 14C10	Cell Signaling Technology	Cat# 2118, RRID:AB_561053
Rabbit monoclonal anti-ACE2	Abcam	ab239924
Rabbit monoclonal anti-Phospho-TBK1(Ser172)	Cell Signaling Technology	Cat# 5483, RRID:AB_10693472
Mouse monoclonal anti-STAT1	BD Biosciences	Cat# 558537, RRID:AB_647231
Rabbit polyclonal anti-MX1	Abcam	ab207414
Mouse monoclonal anti-SARS-CoV-2 Spike [2B3E5]	Center for Therapeutic Antibody Discovery at the Icahn School of Medicine at Mount Sinai	N/A
Mouse monoclonal anti-SARS-CoV-2 Nucleocapsid [1C7C7]	Center for Therapeutic Antibody Discovery at the Icahn School of Medicine at Mount Sinai	N/A
IRDye 680RD Goat anti-Rabbit IgG	LI-COR Biosciences	Cat# 926-68071, RRID:AB_10956166
IRDye 680RD Goat anti-Mouse IgG	LI-COR Biosciences	Cat# 926-68070, RRID:AB_10956588
IRDye 800CW Goat anti-Rabbit IgG	LI-COR Biosciences	Cat# 926-32211, RRID:AB_621843
IRDye 800CW Goat anti-Mouse IgG	LI-COR Biosciences	Cat# 926-32210, RRID:AB_621842
Bacterial and Virus Strains
Ad-mCherry	Vector Biolabs	Cat# 1767
Ad-GFP-h-ACE2	Vector Biolabs	Cat# ADV-200183
SARS-CoV-2 Isolate USA-WA1/2020	BEI Resources	Cat# NR-52281
Influenza A/Puerto Rico/8/1934 (H1N1) virus	Langlois et al., 2013	N/A
Influenza A/California/04/2009 (pH1N1) virus	Langlois et al., 2013	N/A
Influenza A/Texas/71/2017 (H3N2) virus	Langlois et al., 2013	N/A
Influenza A/Puerto Rico/8/1934-ΔNS1 (H1N1) virus	García-Sastre et al., 1998	N/A
rgRSV[224] (strain A2)	Hallak et al., 2000	N/A
rHPIV3JS-GlucP2AeGFP	Blanco-Melo et al., 2020	N/A
Biological Samples
Healthy human lung tissue	Mount Sinai Institutional Biorepository and Molecular Pathology Shared Resource Facility	N/A
COVID-19 human lung tissue	Weill Cornell Medicine	N/A
Human patient sera	Kaiser Santa Clara testing facility	N/A
Chemicals, Peptides, and Recombinant Proteins
Ruxolitnib	ACT Chemical	Cat# ACT06813
Universal Type I IFN	R&D Systems	Cat# 11200-2
Human IFNβ	BEI Resources	Cat# NR-3080
TRIzol Reagent	Thermo Fisher Scientific	Cat# 15596026
Critical Commercial Assays
Direct-zol RNA MiniPrep kit	Zymo Research	Cat# R2051
TruSeq RNA Library Prep Kit v2	Illumina	Cat# RS-122-2001
TruSeq Stranded mRNA Library Prep Kit	Illumina	Cat# 20020594
KAPA SYBR FAST qPCR Master Mix Kit Universal	Kapa Biosystems	Cat# KK4601
VeriKine-HS human IFN-β serum ELISA kit	PBL Interferon Source	Cat# 41415-1
VeriKine-HS human IFN-λ 1/2/3 serum ELISA kit	PBL Interferon Source	Cat# 61840-1
Deposited Data
Raw and analyzed data	This paper	GEO: GSE147507
SARS-CoV-1 and MERS-CoV data	NCBI GEO	GEO: GSE56192
Experimental Models: Cell Lines
A549	ATCC	Cat# CCL-185, RRID:CVCL_0023
Calu-3	ATCC	Cat# HTB-55, RRID:CVCL_0609
Hep-2	ATCC	Cat# CCL-23, RRID:CVCL_1906
MDCK	ATCC	Cat# CCL-34, RRID:CVCL_0422
MDCK-NS1	García-Sastre et al., 1998	MDCK-NS1
Vero E6	ATCC	Cat# CRL-1586, RRID:CVCL_0574
NHBE	Lonza	Cat# CC-2540, #580580
Experimental Models: Organisms/Strains
Ferrets	Triple F. Farm	Fitch ferrets
Oligonucleotides
h-aTubulin_F: GCCTGGACCACAAGTTTGAC	This paper	N/A
h-aTubulin_R: TGAAATTCTGGGAGCATGAC	This paper	N/A
h-IFNb_F: GTCAGAGTGGAAATCCTAAG	This paper	N/A
h-IFNb_R: ACAGCATCTGCTGGTTGAAG	This paper	N/A
SARSCoV2-nsp14_F: TGGGGYTTTACRGGTAACCT	Chu et al., 2020	N/A
SARSCoV2-nsp14_R: AACRCGCTTAACAAAGCACTC	Chu et al., 2020	N/A
SARSCoV2-E_F: ACAGGTACGTTAATAGTTAATAGCGT	Corman et al., 2020	N/A
SARSCoV2-E_R: ATATTGCAGCAGTACGCACACA	Corman et al., 2020	N/A
Software and Algorithms
Prism8	GraphPad	http://www.graphpad.com
ImageStudio	LI-COR	https://www.licor.com/bio/image-studio/
BaseSpace	Ilumina	http://basespace.illumina.com/dashboard
RNA-Seq Aligment App v2.0.2	Ilumina	http://basespace.illumina.com/dashboard
RNA-Express v1.1.10	Ilumina	http://basespace.illumina.com/dashboard
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
STRING	Szklarczyk et al., 2019	https://string-db.org/
gplots	CRAN	https://cran.r-project.org/web/packages/gplots/index.html
PMA	Witten et al., 2009	https://cran.r-project.org/web/packages/PMA/index.html
ggplot2	Tidyverse	https://ggplot2.tidyverse.org/
Bowtie2	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
ImmGen	Yoshida et al., 2019	http://www.immgen.org/