Table 1.
Genes with conditionally changed expression.
| Conditional change | Genes significantly up | Genes significantly down |
|---|---|---|
| Comparisons between genotypes: | ||
| Col_WT vs. atml1-3 | 1 | 1 |
| Col_WT vs. lgo-2 | 5 | 10 |
| atml1-3 vs. lgo-2 | 1 | 13 |
| LGOoe vs. Col_WT | 132 | 24 |
| LGOoe vs. atml1-3 | 305 | 57 |
| LGOoe vs. lgo-2 | 392 | 132 |
| LGOoe atml1-3 vs. Col_WT | 228 | 82 |
| LGOoe atml1-3 vs. atml1-3 | 203 | 89 |
| LGOoe atml1-3 vs. lgo-2 | 584 | 322 |
| LGOoe vs. LGOoe atml1-3 | 25 | 5 |
| Comparisons between batches: | ||
| Batch two vs. batch one | 1,275 | 1,527 |
| Batch three vs. batch one | 1,229 | 1,290 |
| Batch three vs. batch two | 836 | 415 |
For each change between two conditions (genotype or batch, listed as “B vs. A”) and each direction of change (increased or decreased gene expression in B, with respect to A), the number of genes changing expression with statistical significance (as evaluated by DESeq2; see Materials and Methods) is given.