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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

From: A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

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
  1. gyrA and rpoA were used as reference gene
  2. Yellow highlight = Statistically significant, p value ≤0.05