Transcriptome analysis of bovine macrophages (BoMac) cells after infection with bovine immunodeficiency virus

Fig. 1

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Fig. 3

Disease and biofunctions identified by IPA ordered with respect to activation z-score

Diseases or functions annotation	P-value	Activation z-score	Number of molecules
Inflammation of joints	4.61E−09	−3.228*	143
Inflammatory response	1.71E−06	−2.003*	103
Activation of leukocytes	6.71E−07	−1.664	88
Inflammation of respiratory system component	6.93E−06	−1.518	76
Inflammation of body cavity	4.07E−06	−1.467	139
Rheumatoid arthritis	2.18E−07	−1.387	102
Inflammation of lungs	3.60E−06	−1.379	54
Allergic pulmonary eosinophilia	2.95E−06	−1.342	12
Inflammation of organs	1.03E−07	−1.088	187
Inflammation of absolute anatomical region	6.76E−06	−1.049	153
Immune response of tumour cell lines	1.06E−05	−0,788	29
Dermatitis	9.31E−06	−0.363	68

Primers and TaqMan probes used in this study for BIV and GAPDH gene amplification

Primer/Probe	Sequence 5′ → 3′	Position in target sequence	Product length (bp)	Application
BIVg723F	GAAGCAGACATCGAATCAGA	723–742a	552	BIV standard
BIVg1274R	TCTTTTGTGGTTTCTGGAGC	1255–1274 a		DNA
BTG1F	TGATGCTGGTGCTGAGTATGTG	4–25b	182	GAPDH standard
BTG2R	CCTTCAAGTGAGCCTGCAGCAA	164–185 b		DNA
BIVg1074F	ACAAGCCACCCTGATCTCAGTA	1074–1095 a	128	RT-qPCR and
BIVg1202R	TCCTTGGGTTCCCTGATGAATGT	1181–1202 a		qPCR-
BIVg1107P	Cy5 - AACTTTCAGACAGTGGGTGCTGCAGG - BHQ3	1107–1132 a	-	BIV gag gene
BTG3F	CCACTGGGGTCTTCACTACCAT	33–54 b
BTG4R	AAGTTAATTGCACCCGGGCTCT	137–158 b	126	GAPDH qPCR-
BTG5P	JOE - CTGGAGAGGAGGGTGTAACAGGA - BHQ1	83–105 b	-

The top-scoring regulatory networks identified using IPA software

Consistency score	Node total	Regulator total	Regulators	Target total	Target molecules in dataset	Diseases & functions
1.291	20	4	ELF4, INSIG1, INSR, mir-148	15	ACSL1, C1QA, CA2, CD68, CXCL2, DUSP1, FABP4, FDFT1, GABRB3, HSPD1, LDLR, LGALS1, MMP9, PRDM1, VCAM1	Inflammation of joints
−7.211	15	1	INSR	13	ALDH2, CLCA1, DUSP1,EGR1, FABP4,GADD45A, HSPD1, LGALS1, MFN2, MMP9, PRDM1, SERPINB1, VCAM1	Inflammatory response
−7.500	6	1	RABGEF1	4	CTSH, GBA, HEXB, LDLR	Metabolism of protein
−7.506	5	1	ALDH1A2	3	ALDH1A3, CCN2, CD44	Neonatal death
−8.660	5	1	DDX3X	3	CCND1, ODC1, RPS5	Metabolism of protein

Comparison of gene expression changes observed in microarray analysis and RT-qPCR

Gene	Reference sequence ID	Primer sequence (5′–3′)	FC
			Microarray	RT-qPCR
UCHL5*	174481* NM_	F: ACAAAGACAACTTGCTGAGGAACCC	N/A	N/A
		R: GGCAACCTCTGACTGAATAGCACTT
ATR	XM_002685057.2	F: AATGCACGTGTCCTTCGATA	2.45	1.05
		R: TGAAAAGGCCAAGACTCATGT
LTA	NM_001013401.2	F: CCCTCAGAGCCTCGCTTT	2.00	1.19
		R: GCGAGACATCAGAAGAAAGAGC
IL-18	NM_001562	F: AGACAGGTTGATTTCCCTGGT	−1.50	−1.15
		R: CCTGGAATCAGATCACTTTGG
HYAL2	XM_024982390	F: GCGACCAGAGGGGGAACTC	−1.50	−1.03
		R: TAGCACTGGCAGCGAAAGTGCA
		F: TGGTGGAGACTGCCTGCG
DCTN6	XM_024986251	R: CCGACTAAAGAGGTTCTAGCAC	3.00	1.12