De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

Polinski, Mark P.; Bradshaw, Julia C.; Inkpen, Sabrina M.; Richard, Jon; Fritsvold, Camilla; Poppe, Trygve T.; Rise, Matthew L.; Garver, Kyle A.; Johnson, Stewart C.

doi:10.1186/s12864-016-3196-y

Table 1 RNA-seq analysis of Sockeye salmon head kidney transcriptomes in response to PRV and IHNV challenge

From: De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

Time point	PRV challenge & kidney status	IHNV challenge & kidney status	Library name	Accession	Raw reads	Surviving (%)
Group 1 [6 of 11]
14 dpc PRV	Mock injected; PRV-	Not challenged	S86d14nHK	SRX1733826	71,073,165	65,851,201 (93)
			S87d14nHK	SRX1733827	67,245,066	61,789,431 (92)
			S88d14nHK	SRX1733828	70,681,709	65,014,139 (92)
			S89d14nHK	SRX1733829	71,447,579	65,600,555 (92)
			S91d14nHK	SRX1733830	64,978,759	61,093,604 (94)
			S92d14nHK	SRX1733831	66,681,946	60,949,173 (91)
Group 2 [6 of 12]
14 dpc PRV	PRV injection; PRV+	Not challenged	S103d14pHK	SRX1733832	69,883,741	64,413,986 (92)
			S104d14pHK	SRX1733833	72,924,197	68,348,422 (94)
			S105d14pHK	SRX1733834	74,979,891	69,788,197 (93)
			S106d14pHK	SRX1733835	73,571,988	68,612,747 (93)
			S107d14pHK	SRX1733836	68,838,981	64,977,854 (94)
			S108d14pHK	SRX1733837	60,186,123	57,101,607 (95)
Group 3 [4 of 4]
21 dpc PRV (7 dpc IHNV)	Mock injected; PRV-	Mock immersion; IHNV-	SM928d21nHK	SRX1733838	66,335,529	62,802,984 (95)
			SM929d21nHK	SRX1733839	67,164,004	62,826,291 (94)
			SM930d21nHK	SRX1733840	82,046,060	77,026,671 (94)
			SM931d21nHK	SRX1733841	70,537,334	66,494,922 (94)
Group 4 [4 of 8]
21 dpc PRV (7 dpc IHNV)	Mock injected; PRV-	IHNV immersion; IHNV-	S194d21nHK	SRX1733842	70,095,033	66,369,408 (95)
	Mock injected; PRV-	IHNV immersion; IHNV-	S195d21nHK	SRX1733843	67,157,595	63,977,824 (95)
			S197d21nHK	SRX1733844	71,994,014	68,166,660 (95)
			S203d21nHK	SRX1733845	50,101,150	47,036,872 (94)
Group 5 [4 of 4]
21 dpc PRV (7 dpc IHNV)	Mock injected; PRV-	IHNV immersion; IHNV+	S193d21nHKIHN	SRX1733846	79,273,511	75,681,360 (95)
	Mock injected; PRV-	IHNV immersion; IHNV+	S199d21nHKIHN	SRX1733847	76,263,972	72,360,305 (95)
			S200d21nHKIHN	SRX1733851	79,506,752	74,578,577 (94)
			S201d21nHKIHN	SRX1733862	78,032,333	74,005,961 (95)
Group 6 [4 of 4]
21 dpc PRV (7 dpc IHNV)	PRV injection; PRV+	Mock immersion; IHNV-	SM932d21pHK	SRX1733881	67,630,420	64,227,495 (95)
			SM933d21pHK	SRX1733897	73,000,502	69,415,730 (95)
			SM934d21pHK	SRX1733920	83,809,559	79,117,126 (94)
			SM935d21pHK	SRX1733933	64,948,232	61,072,090 (94)
Group 7 [4 of 8]
21 dpc PRV (7 dpc IHNV)	PRV injection; PRV+	IHNV immersion; IHNV-	S206d21pHK	SRX1733942	68,443,344	64,815,041 (95)
			S209d21pHK	SRX1733943	67,232,098	63,015,730 (94)
			S211d21pHK	SRX1733944	70,212,619	65,656,348 (94)
			S213d21pHK	SRX1733945	75,015,092	70,950,399 (95)
Group 8 [4 of 4]
21 dpc PRV (7 dpc IHNV)	PRV injection; PRV+	IHNV immersion; IHNV+	S207d21pHKIHN	SRX1733946	73,284,580	69,850,430 (95)
			S210d21pHKIHN	SRX1733947	68,951,128	65,368,893 (95)
			S214d21pHKIHN	SRX1733948	68,150,625	64,986,061 (95)
			S216d21pHKIHN	SRX1733949	72,009,581	67,717,231 (94)

Libraries are organized into eight groups respective of unique experimental treatment, time points sampled and kidney infection status by both PRV and IHNV as assessed by qPCR. Associated libraries, NCBI SRA accession and sequencing coverage are provided in each instance. The numbers in brackets next to the group identifications indicate the number of samples screened by RNA-seq out of the total number of collected experimental samples available for that condition

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