Innate immune response to a H3N2 subtype swine influenza virus in newborn porcine trachea cells, alveolar macrophages, and precision-cut lung slices

Mario Delgado-Ortega; Sandrine Melo; Darsaniya Punyadarsaniya; Christelle Ramé; Michel Olivier; Denis Soubieux; Daniel Marc; Gaëlle Simon; Georg Herrler; Mustapha Berri; Joëlle Dupont; François Meurens

doi:10.1186/1297-9716-45-42

Table 1

Primer sequences, annealing temperatures of primer sets (°C), expected PCR fragment sizes (bp) and accession numbers or references

Primer name	Primer sequence	Annealing temperature (s) (°C)	PCR product (bp)	Accession number or reference
*ActB*	CACGCCATCCTGCGTCTGGA	63	100	[38]
Beta actin	AGCACCGTGTTGGCGTAGAG	63	100	[38]
*B2MI*	CAAGATAGTTAAGTGGGATCGAGAC	58	161	[38]
Beta-2-microgobulin	TGGTAACATCAATACGATTTCTGA	58	161	[38]
*CISH*	GGGAATCTGGCTGGTATTGG	62	126	BE014034
Cytokine-inducible SH2-containing protein	CCGACAGTGTGAACAGGTAG	62	126	BE014034
*GAPDH*	CTTCACGACCATGGAGAAGG	63	170	AF017079
Glyceraldehyde-3-phosphate dehydrogenase	CCAAGCAGTTGGTGGTACAG	63	170	AF017079
*HMBS-2*	AGGATGGGCAACTCTACCTG	58	83	[38]
Hydroxymethylbilane synthase 2	GATGGTGGCCTGCATAGTCT	58	83	[38]
*HPRT-1*	GGACTTGAATCATGTTTGTG	60	91	[38]
Hypoxanthine phosphoribosyltransferase 1	CAGATGTTTCCAAACTCAAC	60	91	[38]
*IL-1β*	AGAAGAGCCCATCGTCCTTG	62	139	NM_001005149
Interleukine 1 beta	GAGAGCCTTCAGCTCATGTG	62	139	NM_001005149
*IL-6*	ATCAGGAGACCTGCTTGATG	62	177	NM_214399
Interleukine 6	TGGTGGCTTTGTCTGGATTC	62	177	NM_214399
*IL-8*	TCCTGCTTTCTGCAGCTCTC	62	100	NM_213867
Interleukine 8	GGGTGGAAAGGTGTGGAATG	62	100	NM_213867
*IFNα (1-17)*	GGCTCTGGTGCATGAGATGC	64	197	[39]
Interferon alpha (Type I)	CAGCCAGGATGGAGTCCTCC	64	197	[39]
*IFNβ*	ATGTCAGAAGCTCCTGGGACAGTT	62	246	[39]
Interferon beta (Type I)	AGGTCATCCATCTGCCCATCAAGT	62	246	[39]
*IFNγ*	GCTCTGGGAAACTGAATGAC	60	167	NM_213948
Interferon gamma (Type II)	TCTCTGGCCTTGGAACATAG	60	167	NM_213948
*IFNλ1/IL-29A*	GAGGCTGAGCTAGACTTGAC	60	115	NM_001142837
Interferon lambda1 (Type III)	CCTGAAGTTCGACGTGGATG	60	115	NM_001142837
*IFNλ3/IL-28B*	GGCTCCTTGGCGAACTCATC	62	173	GQ996936
Interferon lambda3 (Type III)	TCCTTCTTCTGGGCCTCCTG	62	173	GQ996936
*iNOS*	GAGAGGCAGAGGCTTGAGAC	62	178	BI344008
Inducible nitric oxide synthase	TGGAGGAGCTGATGGAGTAG	62	178	BI344008
*Mx1*	AGTGTCGGCTGTTTACCAAG	60	151	NM_214061
Myxovirus resistance 1	TTCACAAACCCTGGCAACTC	60	151	NM_214061
*Mx2*	CCGACTTCAGTTCAGGATGG	62	156	AB258432
Myxovirus resistance 2	ACAGGAGACGGTCCGTTTAC	62	156	AB258432
*OAS1*	CCCTGTTCGCGTCTCCAAAG	64	303	NM_214303
2′-5′-Oligoadenylate synthetase 1	GCGGGCAGGACATCAAACTC	64	303	NM_214303
*SIV M protein*	AGATGAGTCTTCTAACCGAGGTCG	62	100	[40]
*SIV M protein*	TGCAAAAACATCTTCAAGTCTCTG	62	100	[40]
*PKR*	GACATCCAAAGCAGCTCTCC	62	365	NM_214319
Protein Kinase RNA-dependent	CGCTCTACCTTCTCGCAATC	62	365	NM_214319
*RPL-19*	AACTCCCGTCAGCAGATCC	60	147	[41]
Ribosomal protein L19	AGTACCCTTCCGCTTACCG	60	147	[41]
*RIG-I*	CGACATTGCTCAGTGCAATC	60	126	NM_213804
Retinoic acid-inducible gene I	TCAGCGTTAGCAGTCAGAAG	60	126	NM_213804
*SDHA*	CTACAAGGGGCAGGTTCTGA	58	141	[38]
Succinate dehydrogenase complex subunit A	AAGACAACGAGGTCCAGGAG	58	141	[38]
*SOCS1*	CGCCCTCAGTGTGAAGATGG	62	110	EW101597
Suppressor of cytokine signaling 1	GCTCGAAGAGGCAGTCGAAG	62	110	EW101597
*SOCS3*	CAGCTCCAAGAGCGAGTACC	61	179	NM_001123196
Suppressor of cytokine signaling 3	TGACGCTGAGCGTGAAGAGG	61	179	NM_001123196
*TBP-1*	AACAGTTCAGTAGTTATGAGCCAGA	60	153	[38]
TATA box binding protein 1	AGATGTTCTCAAACGCTTCG	60	153	[38]
*TLR3*	CCTGCATTCCAGAAGTTGAG	60	152	NM_001097444
Toll Like Receptor 3	TGAGGTGGAGTATTGCAGAG	60	152	NM_001097444
*TLR7*	TCAGCTACAACCAGCTGAAG	60	140	NM_001097434
Toll Like Receptor 7	CAGATGTCGCAACTGGAAAG	60	140	NM_001097434
*TLR8*	AGCGCGGGAGGAGTATTGTG	62	118	NM_214187
Toll Like Receptor 8	GCCAGGGCAGCCAACATAAC	62	118	NM_214187
*TNFα*	CCAATGGCAGAGTGGGTATG	62	116	X54859
Tumor Necrosis Factor alpha	TGAAGAGGACCTGGGAGTAG	62	116	X54859

Reference genes are in italic.