Table 3 Comparison of fold change (Minus vs KCL-supplemented treatment) RT-qPCRs and Transcriptomes of E. coli. Please note that the genes analyzed for this validation study are based on DNAstar-D regulated genes since we found it to be the most conservative pipeline. The transcriptome data shown are ≥ 1.5 fold cutoff
Target | Fold change | ||||||
|---|---|---|---|---|---|---|---|
RT-PCR | Transcriptome | ||||||
REST | CFX | Qbase+ | DNAstar-D | DNAstar-E | CLC | Partek | |
sodA | 1.6 | 1.4 | 1.4 | 1.9 | 2.8 | 2.7 | 3.0 |
yhiD | -1.2 | -1.3 | -1.3 | -2.7 | -5.5 | -5.5 | -5.7 |
zrsA | 1.1 | 1.0 | 1.0 | ND | ND | ND | ND |
citF | -1.4 | -1.5 | -1.5 | -2.2 | -8.5 | -8.4 | -8.6 |
cysH | -1.1 | -1.2 | -1.2 | -3.4 | -5.8 | -5.7 | -5.2 |
hycF | -1.0 | -1.0 | -1.0 | -2.0 | -4.5 | -4.8 | -4.2 |
appA | -1.2 | -1.3 | -1.3 | -2.2 | -7.5 | -7.5 | -7.7 |
mdtF | -1.0 | -1.1 | -1.1 | -3.4 | -6.7 | -6.7 | -6.9 |
ydhW | -1.2 | -1.3 | -1.3 | -2.3 | -3.8 | -3.5 | -3.8 |
cheY | 1.4 | 1.5 | 1.3 | 1.6 | 1.6 | 1.5 | 1.6 |
motA | 1.6 | 1.4 | 1.4 | 1.7 | 1.8 | 1.7 | 1.8 |
napA | 1.4 | 1.3 | 1.3 | 2.3 | 9.1 | 9.1 | 8.7 |
fhuA | 1.9 | 1.6 | 1.6 | 2.1 | 3.4 | 3.2 | 3.1 |
fliZ | 1.7 | 1.5 | 1.5 | 2.1 | 2.4 | 2.4 | 2.4 |
gadC | 1.4 | 1.3 | 1.3 | -2.5 | -16.9 | -16.9 | -16.7 |
nirB | 2.5 | 2.2 | 2.2 | 2.1 | 4.8 | 4.6 | 4.4 |
cyoC | 4.3 | 3.9 | 3.9 | 2.2 | 5.0 | 5.0 | 5.5 |
efeO | 1.5 | 2.3 | 2.2 | 1.9 | 3.0 | 2.9 | 3.0 |
hyaB | 2.0 | 1.7 | 1.7 | -2.1 | -7.8 | -7.7 | -7.5 |
cysI | -1.2 | -1.3 | -1.3 | -2.5 | -5.5 | -5.7 | -6.0 |
slp | -1.7 | -2.0 | -2.0 | -2.1 | -12.8 | -12.8 | -12.8 |
mdtF | -1.1 | -1.1 | -1.1 | -2.5 | 8.0 | -6.7 | -6.9 |