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To establish the reproducibility of the ChIP-chip replicates, correlation analysis of log2 ChIP/Input ratios between replicates was done with values resulting from MaxSixty calculations.
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Comparisons of curves both among groups [(resistant (exposed and uninfected), susceptible (exposed and infected), and unexposed (fed on uninfected chicken)] and between replicates were done with a log-rank test, which is equivalent to the Mantel-Haenszel test.
Three replicates were done for each sample.
Two replicates were done for each diet.
Two biological replicates were done for each sample.
One hundred bootstrap replicates were done in Paup [49] version 4.0d105.
Three biological and technical replicates were done for each sample.
Biological and technical replicates were done in triplicate.
Two biological replicates were done.
Three independent biological replicates were done.
Three replicates corresponding to independent experiments (biological replicates) were done for each treatment/genotype.
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