Table 3.

CRISPR KO datasets used for validating predicted synthetic lethal targets.

Study	Cell line	Library	Virus strain	MOI	DPI	N depleted gene products
SARS-CoV-2
Biering	Calu3ACE2/TMPRSS2	Brunello	USA-WA1/2020	0.05	4	0
Baggen	Huh7	Brunello	USA-WA1/2020	2.5, 0.1	41, 22	0
Daniloski	A549ACE2	GeCKOv2	USA-WA1/2020	1	6	0
		A&B		3	6	0
Rebendenne	Caco2ACE2	Brunello	BetaCoV/France/IDF0372/2020	0.005	10-13	206
	Calu3	Gattinara	BetaCoV/France/IDF0372/2020	0.005	10-13	0
Schneider	Huh7.5 at 33°C	Brunello	USA-WA1/2020	0.01	5	63
	Huh7.5 at 37°C			0.1	5	73
Wang	Huh7.5ACE2/TMPRSS2	GeCKO	USA-WA1/2020	0.01	12	3
Zhu	A549ACE2	Brunello	SARS-CoV-2/human/CHN/SH01/2020 (nCoV-SH01)	3	7+	12
Hou	A549ACE2	H1	rec. 2019-nCoV/USA_WA1	5	2	84
Grodzki	HEK239ACE2 – initial infect	Brunello	UF-1	0.01	(40% CPE)	627
	HEK239ACE2 - reinfect			0.01	(40% CPE)
	HEK239ACE2 - reinfect			0.1	(40% CPE)
Israeli	Calu3	Brunello	B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta)	0.02-0.04	7-9	7
Hoffmann	Huh7.5 at 33°C	custom$	USA-WA1/2020	0.25	7	19
	Huh7 .5 at 37°C			0.25	11	21
Influenza
Han J, Cell Rep., 2018	A549	GeCKO	H5N1 (VNO4LOW)	5	2(rd 2)	0
Yi C, Cell Rep., 2022	A549	GeCKO	H7N9 H7N9 (A/chicken/Guangxi/97/2017)	0.01	10 (after 2 rds)	26
Tran V, Synthego, 2020	A549	GeCKO	H1N1 (IAV-G, pseudotyped A/WSN/1933 strain)	0.3	20-21 (rd 1)	1
		GeCKO	H1N1 (A/WSN/1933)	0.3	40-42 (rd 2)	2
		Brunello	H7N7 (SC35M Flu-GFP; A/seal/Massachusetts/1-SC35M/1980)	0.1	63 (after 7 rds)	1669

Significance cut-offs: L2FC < 0, FDR < 0.05 (Biering, Baggen Daniloski, Wang, Zhu, Hou, Grodzki, Israeli) or z-score < −1.96 (Rebendienne, Schneider, Hoffman)

^$“Human SARS-COV-2 host protein interactome CRISPR library” including sgRNAs targeting 332 host factor proteins interacting with SARS-COV-2 proteins and control sgRNAs

^#Influenza-virus infected cells were generally allowed to expand after each round of infection

MOI: multiplicity of infection; DPI: days post-infection, rd(s): round(s) of infection