TABLE 1.

Top 20 upregulated DEGs when compared with mock-infected cells.

	IAV vs. mock		IBV vs. mock		RV vs. mock
Hours post-infection	Gene name	log2 (Fold Change)	Gene name	log2 (Fold Change)	Gene name	log2 (Fold Change)
12	IFNL2	7.10	IFNL1	9.88	IFNL2	7.61
	IFNL1	7.09	CXCL10	9.63	IFNL3	7.38
	IFNL3	6.89	IFNL2	9.55	IFNB1	7.34
	RSAD2	6.76	IFNL3	9.36	IFNL1	7.14
	CXCL10	6.68	IFNB1	8.95	AC011511.5	6.13
	IFNB1	6.44	CXCL11	8.91	FAP	6.01
	IDO1	6.28	IDO1	8.59	TULP2	5.77
	BATF2	6.19	CCL5	8.40	RPL7P19	5.51
	MX2	5.92	BATF2	8.14	ZBP1	5.38
	IFIT2	5.86	GBP5	8.09	AL133163.1	5.36
	OAS2	5.76	CXCL9	8.01	ICAM5	5.25
	OR52K3P	5.58	RSAD2	7.89	CXCL10	5.12
	IFIT3	5.53	GBP4	7.70	RSAD2	5.02
	AC005515.1	5.53	ZBP1	7.42	BATF2	4.65
	IFIT1	5.52	CX3CL1	7.33	IFIT2	4.63
	GBP4	5.52	AC005515.1	7.24	MX2	4.61
	TRIM22	5.43	LRP2	7.18	IFIT1	4.48
	ZBP1	5.40	MX2	7.10	OAS2	4.46
	ETV7	5.40	CD69	6.99	IFIT3	4.35
	CMPK2	5.39	CSF3	6.94	CMPK2	4.31
24	CXCL10	10.32	CXCL10	12.08	CXCL10	8.90
	CXCL11	9.20	CXCL11	11.58	IFNL3	7.68
	ZBP1	9.01	IFNL1	10.44	IFNL2	7.62
	IDO1	8.56	CCL5	10.35	CXCL11	7.59
	IFNL2	8.31	CSF3	10.21	ZBP1	7.45
	KLHDC7B	8.26	IFNL2	10.07	RSAD2	7.21
	IFNL3	8.21	IFNL3	9.90	MX2	7.13
	IFNL1	8.11	TNF	8.97	IFNL1	6.92
	RSAD2	7.98	RSAD2	8.79	IDO1	6.90
	TRIM22	7.76	IFNB1	8.76	OAS2	6.89
	SLC15A3	7.69	IL6	8.73	TRIM22	6.79
	MX2	7.64	ZBP1	8.41	CMPK2	6.77
	CCL5	7.55	IDO1	8.33	IFNB1	6.71
	BST2	7.48	AL021578.1	8.28	KLHDC7B	6.53
	OAS2	7.27	CX3CL1	8.12	SLC15A3	6.47
	GBP4	7.21	HSPA6	8.04	GBP4	6.09
	AC005515.1	7.13	CXorf49B	7.84	FAP	6.01
	CX3CL1	7.01	OASL	7.83	ETV7	5.82
	CMPK2	6.94	GBP4	7.82	BST2	5.82
	ETV7	6.82	CCL22	7.71	BATF2	5.77

The log2 fold changes are based on MRN normalization (cf. Supplementary Data S3).