Table 2.

RNA-Seq analysis of fish in response to viral pathogens. This table shows a description of transcriptomes to understand viral diseases in various fish species.

Sl No	Fish	Virus	Sample	Sequencing Platform	Sequencing Depth/Library	Accession Number	Reference
1	Rainbow trout	Poly I:C (viral mimic)	Erythrocytes	ABI SOLiD3	80 M *,a	NA	[66]
2	Large yellow croaker	Poly I:C (viral mimic)	Spleen	Illumina Genome Analyzer II	56.3 M	SRP035897	[67]
3	Rainbow trout	Viral Hemorrhagic Septicemia Virus	Spleen & rayed fin	Illumina HiSeq 2000	3.119 B	NA	[68]
4	Grass carp	Grass carp reovirus	Gill, intestine, liver & spleen	Illumina HiSeq 2000	203 M	SRA099702	[69]
5	Atlantic salmon	Infectious salmon anaemia virus	Head kidney, liver & gills	Illumina MiSeq	196 M	SRX658605	[70]
6	Grass carp	Grass carp reovirus	Head kidney & spleen	Illumina MiSeq	107.9 M *	SRP049081	[71]
7	Miiuy croaker	Poly I:C (viral mimic)	Spleen	Illumina HiSeq 2000	Control: 50.3 M *	NA	[72]
					Treated: 48.2 M *
8	Grass carp	Grass carp reovirus	Spleen	Illumina HiSeq 2000	Control: 2.72 M *	NA	[73]
					Infected: 2.75 M *
9	Olive flounder	Heat inactivated viral hemorrhagic septicemia virus	Kidney	Illumina HiSeq 2500	Control: 23.7 M *	NA	[74]
					Day 1: 24.4 M *
					Day 3: 23.8 M *
					Day 7: 25.9 M *
10	Atlantic salmon	Infectious salmon anaemia virus	Spleen	Illumina MiSeq	92.8 M *	NA	[75]
11	Schizothorax	Poly I:C (viral mimic)	Spleen	Illumina Hiseq 2500	Control: 53.8 M *	NA	[76]
					Treated: 55.1 M *
12	Orange spotted grouper	Megalocytivirus and Ranavirus	Spleen	Illumina HiSeq	NA	NA	[77]
13	Grouper	Betanodavirus	Kidney cell line	Illumina HiSeq 2000	51 M	JR139431–JR139455	[78]
						JX644070
14	Sockeye salmon	Piscine reovirus along with superinfection of infectious hematopoietic necrosis virus	Kidney	Illumina HiSeq 2000	2.3 B	SRP0740078	[79]
15	Atlantic salmon	Salmonid	TO-cells, a macrophage/dendritic like cell line	Illumina HiSeq 2000	Interferon treated: 23.1 M *	GSE64095	[80]
					SAV3 infection: 24.6 M *
		alphavirus subtype-3			Control: 23.4 M *
16	Gilthead seabream & European seabass	Nervous necrosis virus (Betanodavirus)	Leucocytes	Illumina HiSeq 2000	53 M a	GSE101662	[81]
17	Koi carp	Cyprinid Herpesvirus 3	Spleen	Illumina HiSeq 2500	111.2 M	NA	[82]
18	Yellow catfish	Poly I:C (viral mimic)	Liver	Illumina HiSeq 2000	Control: 42.2 M *	NA	[83]
					Treated: 41.5 M *
19	Zebrafish	Spring viremia of carp virus	Brain & spleen	Illumina HiSeq 4000	360.9 M *	NA	[84]
20	Olive flounder	Viral hemorrhagic septicemia virus	Kidney	Illumina HiSeq 2000	215.8 M	NA	[85]
21	Orange spotted grouper	Singapore grouper iridovirus	Spleen	Roche 454 Genome	Control: 0.428 M	SRA040065.1	[86]
				Sequencer FLX	Infected: 0.446 M
22	Turbot	Megalocytivirus	Spleen	Illumina HiSeq 2000	S16-4d: 82.9 M	SAMN06186733 to SAMN06186736	[87]
					S16-8d: 86.5 M
					S16-4d: 81.4 M
					S16-4d: 79.1 M

* Clean reads; NA—Not available; M—Million reads; B—Billion reads; ^a—Average read values.