Fig. 7

Assessment of the PCR1 products. A Assessment of gene expression levels in the PCR1 product. Actual vs. predicted gene expression levels of a set of five genes were assessed in the long-term infection samples via qPCR. PCR1 products from each long-term goat sample were amplified with five primer sets for the ndvB, ribE, dksA, entA, and eryK genes, as described in “Methods”. ΔC_t values were calculated for the expression of each gene relative to the expression level of the entA gene. The relative gene expression is expressed here as the log₂ (expression level of gene of interest/expression level of entA), with closed squares for the qPCR-derived differences in expression and closed circles for the RNA-Seq-derived differences in expression (genes with higher expression than entA are depicted as positive values in this figure). Values were averaged across all four long-term goat samples (four biological replicates) to obtain the data points. B Assessment of suppression in the PCR1 reaction. PCR1 templates from three different tissue-derived samples (lanes 1–3, lanes 4–6, and lanes 7–9) were amplified under the PCR2 reaction parameters (described in “Methods”) with either Not1Srf primer (marked as “a”), Not1Rsa primer (marked as “b”), or both primers (marked as “a + b”). NC = negative control reaction, with no template but both primers. Numbers indicated on the left side of the gel indicate the molecular weight of ladder bands in base pairs