Table 2.

Analysis matrix for sheep B cell-related gene expression in intestinal tissue for specific research questions

Research question	Baseline group	Comparison group (s)
Q1. What gene expression changes are associated with disease outcome in non-vaccinated animals? Are these similar in vaccinated animals?	Non-vaccinated control	Non-vaccinated infected Non-vaccinated uninfected Vaccinated infected Vaccinated uninfected
Q2. What gene expression changes are associated with disease outcome in vaccinated animals	Vaccinated control	Vaccinated infected Vaccinated uninfected
Q3. What gene expression changes are associated with infection in vaccinated animals	Vaccinated uninfected	Vaccinated infected
Q4. What gene expression changes are associated with vaccination nonresponse in infected animals	Non-vaccinated infected	Vaccinated infected