REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Fam98A	Aviva	ARP55 265_P050; RRID:AB_2045839
Tubulin	Sigma	T9026; RRID:AB_477593
CGI-99(C14orf166)	Atlas antibodies	HPA039824; RRID:AB_10793922
dsRNA	Jena Bioscience	RNT-SCI-10010200; RRID:AB_2651015
SARS-CoV2 Nucleocapsid	Sino Biological	AB 40143-MM05; RRID:AB_2827977
HNRNPA1	Cusabio	CSB-PA00109A0Rb
rabbit Alexa Fluor 488	Thermo Fischer	#A-11008; RRID:AB_143165
mouse Alexa Fluor 647	Thermo Fischer	#A-21235; RRID:AB_2535804
DDX1 (immunofluorescence)	Cambridge Bioscience Ltd	HPA034502; RRID:AB_10794321
DDX1 (immunoblotting)	Bethyl	A300-521A; RRID:AB_451046
Bacterial and virus strains
SARS-CoV-2 hCoV-19/England/02/2020	Public Health England propagated viral isolate Feb 2020	EPI_ISL_407073
SARS-CoV-2 hCoV-19/Germany/BavPat1/2020	European Virology Archives: 026V-03883	EPI_ISL_406862
Chemicals, peptides, and recombinant proteins
Ganetespib	BIOZOL	BYT-ORB181166
MS-444	Hycultec	HY100685-1mg
compound 3k	BIOZOL	SEL-S8616
Ro 08-2750	TOCRIS	2272
BTYNB	Cayman Chemical	25623
Deposited data
Proteomic data	This study	PRIDE: PXD023418
NGS data	This study	GEO: GSE171382
NGS data	Blanco-Melo et al., 2020	GEO: GSM4462348 to GEO: GSM4462353
Experimental models: Cell lines
Calu-3	kind gift from Dr. Manfred Frey, Mannheim, Germany	N/A
A549-Ace2	Klein et al., 2020	N/A
Software and algorithms
DESeq2 (1.28.1)	Love et al. (2014)	N/A
ggrepel 0.8.2	(Slowikowski, 2020) https://github.com/slowkow/ggrepel	N/A
GO.db 3.11.4	Carlson, 2019	N/A
htseq-count 0.11.3	(Anders et al., 2015) https://github.com/simon-anders/htseq/releases	N/A
KEGGREST 1.28.0	Tenenbaum and Maintainer, 2021	N/A
limma 3.38.3	Ritchie et al. (2015)	N/A
org.Hs.eg.db 3.11.4	Carlson, 2019	N/A
PerformanceAnalytics 2.0.4	(Peterson and Carl, 2020) https://github.com/braverock/PerformanceAnalytics	N/A
PFAM.db 3.11.4	Carlson et al., 2019	N/A
RBDetect	https://nishuai.shinyapps.io/RBDetect/	N/A
rentrez 1.2.2	(Winter, 2017) https://github.com/ropensci/rentrez/releases	N/A
scales 1.1.1	(Wickham and Seidel, 2020) https://scales.r-lib.org/	N/A
SRA toolkit	SRA Toolkit Development Team. http://ncbi.github.io/sra-tools/	N/A
Stats 4.0.2	R core team https://www.R-project.org/	N/A
tidyverse suite 1.3.0	(Wickham et al., 2019) https://tidyverse.org	N/A
viridis 0.5.1	(Garnier, 2018) https://github.com/sjmgarnier/viridis	N/A
VSN 3.50.0	Huber et al. (2002)	N/A
DEP 1.4.1	Zhang et al. (2018)	N/A