Additional file 2 of Transcriptome analysis of aphid-resistant and susceptible near isogenic lines reveals candidate resistance genes in cowpea (Vigna unguiculata)

Additional file 2: Table S1. Differential coexpression analysis identified clusters (modules: M) of genes that shared expression patterns within treatments but differed between treatments (see Figure 3). Table S2. Alignment statistics for raw reads. Table S3. Contrasts of treatments and associated DEGs at high and low LFC thresholds. Table S4. qRT-PCR validation of select genes differentially expressed in RNAseq data relative to susceptible (CB46) uninfested plants. Genes consistently upregulated across time in resistant cowpea (CB77; A:RGA4-600, B:RGA4-700) and genes differentially expressed among treatments (C:CHiB, D:STE11) showed expression trends in concordance with RNAseq data (*) relative to susceptible control tissues at the collection time point. Primers for select genes are listed (E) and the fit of all expression data to count data showed high correlation (F: R2=0.79).