FIG 2.

Transcriptional response of E. coli exposed to ceragenins. RNA from exponentially growing E. coli bacteria exposed to supra-MICs of colistin (COL), LL37, CSA13, and CSA131 was extracted and sequenced. (A–D) Replica plots showing the log₁₀ of the normalized number of reads per gene for bacteria exposed to antibiotics. Correlation coefficients (R) between replicates #1 and #2 (black dot) and #1 and #3 (red dot) are displayed. (E-H) Volcano plots that represent RNA expression as means of log₂-fold change and -log₁₀ adjusted P values (adj. P value) for bacteria exposed to antibiotics in comparison to untreated control samples. Horizontal and vertical dotted red lines indicate adjusted P values less than 0.05 (or −log₁₀ [adj. P value] greater than 1.3) and absolute log₂-fold change greater than 1. (I) Multidimensional scaling (MDS) plot showing the separation between biological replicates and between untreated and antibiotic-treated samples. (J) Annotation terms enriched for genes significantly upregulated (log₂ FC > 1 and adj. P value <0.05) following exposure to antibiotics. (K) Annotation terms enriched for genes significantly downregulated (log₂ FC <−1 and adj. P value <0.05) following exposure to antibiotics. Adjusted P values of annotation terms associated with a false discovery rate (FDR) value >0.05 for at least one antibiotic are shown. Only the 8 most statistically significant annotation terms are shown for each condition. Annotation terms are abbreviated and/or modified for a purpose of presentation (see Data Set S2 for original annotation terms). Data are from 3 independent experiments.