Table 2.

Number of DEGs in each treatment group (LogFC >1.5, FDR < 0.05).

	Brain			Ileum			Lung
	Time 1	Time 2	Time 3	Time 1	Time 2	Time 3	Time 1	Time 2	Time 3
H9 infection
Chicken	22	15	10	444	394	326	73	12	89
Turkey	451	726	349	53	687	1113	–	–	–
Duck	46	96	17	23	188	31	301	488	572
Crow	36	21	12	186	162	186	133	38	89
Goose	7	0	138	418	636	320	46	4	149
Pigeon	5	3	5	19	65	219	195	9	17
2.2 infection
Chicken	73	223	892	305	275	744	464	1069	2124
Turkey	489	1135	675	697	223	304	–	–	–
Duck	24	95	498	24	141	268	534	790	444
Crow	48	54	16	652	341	228	75	273	113
Goose	294	23	260	331	43	279	71	57	20
Pigeon	6	4	21	10	55	93	94	37	348
2.3.2.1 infection
Chicken	23	147	1342	238	1301	1930	266	596	1902
Turkey	36	372	1167	214	939	1500	–	–	–
Duck	46	360	607	10	275	406	100	822	402
Crow	21	19	38	54	117	116	249	319	204
Goose	86	237	245	121	326	161	17	68	32
Pigeon	13	12	5	23	26	33	45	67	34

Time 1, 2, 3 = 12h, 24h and 48h in chicken and turkey to 2.2 and 2.3 infection. Time 1, 2, 3 = 12h, 48h and 5d in the remaining treatment groups.