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+## Differential expression analysis
+
+Differentially expressed genes between microbe treatments and mock treatments were identified using Sleuth (Pimentel et al., 2017; Figure S2). The p-values were adjusted using the Benjamini-Hochberg correction (FDR ≤ 0.05; Benjamini and Hochberg, 1995). Since Sleuth relies on replicates within treatments, BioProjects without replicates were removed from this part of analysis. We evaluated differences between i) *R*-genes and all genes, ii) proportion of up- versus down-regulation iii) average absolute fold changes
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