Table 1.
Number of transcriptomic and methylation probes after each step of the microarray design and analysis
| Origin of the sequences | Submitted sequences | Designed probes | Filtered probes | DEGs or DMRs | |
|---|---|---|---|---|---|
| Transcriptomic | Public database | 154 mitochondrial ORFs | 132 | 106 | 2 |
| 30 023 ORFs from ESTs | 28 918 | 21 043 | 159 | ||
| 22 candidate genes | 44 | 26 | 3 | ||
| Cot fraction | 42 004 ORFs | 24 658 | 1273 | 5 | |
| Total | 72 203 | 53 752 | 22 448 | 169 | |
| Methylation | Public database | 1 mitochondrial genome | 3688 | 3211 | 27 |
| 29 585 ESTs | 185 425 | 14 069 | 110 | ||
| 22 candidate genes | 1426 | 109 | 1 | ||
| Cot fraction | 6231 contigs | 36 | 2185 | 0 | |
| Total | 35 839 | 227 242 | 19 574 | 138 |
DEG, differentially expressed gene; DMR, differentially methylated region.
The Cot fraction corresponds to single-copy sequences obtained after Cot filtration and 454 sequencing of sugar beet genomic DNA.
DEGs and DMRs correspond to sequences showing both significantly different signals (t-test analysis with P<0.05 and P<0.01, respectively) and fold change >2 between resistant and sensitive genotypes.