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The six field isolates were included in this experiment, as reference strains are adapted to laboratory growth conditions and hence are expected to be more stable with respect to plasmid-borne genes.
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Ingenuity Pathway Analysis (version 5.5) [ 27] was used to identify functional enrichment in the clusters, using the respective source gene sets (6,149 genes in tissue experiments, 4,711 in liver time-series experiments) as reference.
Six bulls were slaughtered at the beginning of the experiment as the reference group, to estimate initial empty body weight (EBW) and energy and protein contents of the remaining animals.
Six bulls were slaughtered at the beginning of the experiment as a reference group to estimate the initial empty body weight (BW) and energy content of the remaining animals.
Using a recent experiment as the reference, we choose the laser pulse and target so that the energy spectrum obtained from the 3D PIC simulation is close to the one observed, whose cutoff energy was estimated to be over 50 MeV.
PGF2α (10−7 M) was used at the beginning and end of each dose response experiment as a reference compound.
The experiments were conducted in batches under similar growth conditions, and each batch had its own control experiment as a reference.
Model predicted fold-changes were computed the same way as the experimental ones, using the quantity predicted at the first time of the control experiment as a reference.
All fold-changes were calculated using the absolute value measured at the first time of the control experiment as a reference, and for all doses.
For a multigenome array, however, it is not possible to use data from any single hybridization experiment as a reference data set.
To allow comparison of ratios between the two experiments, spot volume data for the two fluorescence channels were first normalized by median normalization (Keeping and Collins, 2011) using the median values for the first experiment as a reference.
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