Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens

Sun, Hongyan; Liu, Peng; Nolan, Lisa K.; Lamont, Susan J.

doi:10.1186/s12864-015-1850-4

BMC Genomics

Table 2 Quantitative PCR validation

From: Avian pathogenic Escherichia coli (APEC) infection alters bone marrow transcriptome in chickens

Gene	Contrast	qPCR	RNA-seq
ADA	Susceptible vs. Non-challenged birds at 5 dpi	−15.66**	−3.92**
	Susceptible vs. Resistant birds at 5 dpi	−18.99**	−3.39**
	5 dpi vs. 1 dpi in susceptible birds	−9.29**	−2.50**
BLNK	Susceptible vs. Non-challenged birds at 5 dpi	+3.11*	+2.50**
	Susceptible vs. Resistant birds at 5 dpi	+4.71**	+2.22*
	5 dpi vs. 1 dpi in susceptible birds	+3.85**	+2.19**
CD3D	Susceptible vs. Non-challenged birds at 1 dpi	−2.36**	−1.67**
CD28	Susceptible vs. Non-challenged birds at 5 dpi	+7.17**	+2.27*
CD40	Susceptible vs. Non-challenged birds at 5 dpi	+4.40**	+2.93**
	Susceptible vs. Resistant birds at 5 dpi	+2.44**	+2.25**
	5 dpi vs. 1 dpi in susceptible birds	+2.25*	+1.91**
CD3Z	Susceptible vs. Non-challenged birds at 1 dpi	−1.91	−1.77**
CD3Z	Susceptible vs. Resistant birds at 5 dpi	−7.05*	−2.11**
IFNG	Susceptible vs. Non-challenged birds at 1 dpi	−2.19**	−1.71*
IL1	Susceptible vs. Non-challenged birds at 5 dpi	+2.41*	+5.21**
IL7	Susceptible vs. Non-challenged birds at 5 dpi	−3.38**	−4.69**
	Susceptible birds vs. Resistant birds at 5 dpi	−1.96*	−3.36*
	5 dpi vs. 1 dpi in susceptible birds	+2.72*	+5.43**
IL8	Susceptible vs. Non-challenged birds at 5 dpi	+6.70**	+6.06**
	Susceptible vs. Resistant birds at 5 dpi	+2.69*	+2.72**
	5 dpi vs. 1 dpi in susceptible birds	+3.89*	+2.37*
IL18	Susceptible vs. Non-challenged birds at 5 dpi	+6.47**	+3.97**
IL18	Susceptible vs. Resistant birds at 5 dpi	+2.40*	+2.82**
LIG4	Susceptible vs. Non-challenged birds at 5 dpi	−6.14**	−1.57*
MD2	Susceptible vs. Non-challenged birds at 5 dpi	+2.39**	+3.10**
	Susceptible vs. Resistant birds at 5 dpi	+2.26**	+2.55**
	5 dpi vs. 1 dpi in susceptible birds	+2.16**	+1.83**
NOD1	Susceptible vs. Non-challenged birds at 5 dpi	+2.77*	+2.17**
NOD1	Susceptible vs. Resistant birds at 5 dpi	+5.36**	+1.97**
TLR4	Susceptible vs. Non-challenged birds at 5 dpi	+3.26**	+2.77**
	Susceptible vs. Resistant birds at 5 dpi	+2.53*	+2.35**
	5 dpi vs. 1 dpi in susceptible birds	+2.75*	+1.89**

Note: Fold change between contrasts presented in third and fourth column. + values indicate higher expression in the first group, − values indicate higher expression in the second group. ** is P value < 0.01 in qPCR or FDR < 0.01 in RNA-seq; * is P value < 0.05 in qPCR or FDR < 0.05 in RNA-seq.

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