Table 2.
Validation of DESeq2 analysis with qRT-PCR of 3 genes with different expression pattern.
| SeqName | ΔCq (a) | ΔCq (b) | ΔΔCq | BaseMean | Log2fold change | Comparison (a):(b) |
|---|---|---|---|---|---|---|
| Ben3g3530 | − 1.92 ± 0.59 | 6.38 ± 0.32 | 8.30* | 451 | 8.93 | (early):(Ben3) |
| − 1.00 ± 0.92 | 6.38 ± 0.32 | 7.37* | 181 | 7.79 | (late):(Ben3) | |
| − 1.92 ± 0.59 | − 1.00 ± 0.92 | − 0.92 | – | n.s | (early):(late) | |
| Ben3g2070 | − 4.17 ± 0.95 | 5.59 ± 0.53 | 9.76* | 1,102 | 9.00 | (early):(Ben3) |
| 0.47 ± 2.03 | 5.59 ± 0.53 | 5.12* | 109 | 5.27 | (late):(Ben3) | |
| − 4.17 ± 0.95 | 0.47 ± 2.03 | − 4.64* | 222 | − 2.29 | (early):(late) | |
| Ben3g4553 | − 5.83 ± 0.29 | n.d | – | 64 | 9.97 | (early):(Ben3) |
| n.d | n.d | – | – | n.s | (late):(Ben3) |
ΔCq, relative expression value calculated as Cqgene − CqTUB2; ΔΔCq, differences in relative expression levels calculated as (ΔCq (b) − ΔCq (a)); *, stands for significant difference of ΔΔCq (n = 3; P ≤ 0.05; t-test); BaseMean, average calculated with DESeq2 package as implemented in the ReadXplorer software; Log2fold change, calculated with the DESeq2 package as implemented in the ReadXplorer software; Comparison, as indicated, pure mycelium of R. solani AG3-PT isolate Ben3 cultured without being attracted by a growing potato plant (Ben3) compared to Ben3 in interaction with potato sprouts at 3 dpi (early) or at 8 dpi (late); Values are given in Supplementary Tables 8–10; n.s., not significant; n.d., not detected.