Fig. 3: smRandom-seq captured transcriptome changes of single E. coli upon antibiotic stress.
From: Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq
a Experimental design for CIP (ciprofloxacin, 15 μg/mL)-treated E. coli samples. b Images of E. coli treated with CIP for 0, 1, 2, and 4 h. n = 4 independent experiments. c UMAP projection of all the bacteria collected at the different time points, based on their gene expression colored by time point. d Violin plot showed the expression levels of outer membrane protein-encoding genes (ompF, tsx, and lamB) in samples. 0 h n = 771 cells, CIP 1 h n = 850 cells, CIP 2 h n = 950 cells, CIP 4 h n = 949 cells. The expression levels of each gene in each cell were normalized, log-transformed (log(1 + x)), and scaled data. The violin plots showed the kernel density estimate of the underlying data. e Mean expression levels of top 5 DEGs among different samples. The color of each dot represents the mean expression within each sample and the size of each dot represents the fraction of cells expressing the DEGs in different samples. f Bubble plots of GO enrichment analysis of top 20 DEGs in CIP 2 h sample. Gene count: the number of DEGs enriched in a GO term. Gene ratio: the number of observed DEGs divided by the number of expected genes from each GO term. The cutoff value of the p-value of GO enrichment was 0.05 and the cutoff value of the q-value of GO enrichment was 0.05. g, h Mean expression levels of genes involved in SOS-response and reactive oxygen species (ROS) degradation (g) and different metabolic pathways (h) in different time point samples. The color of each dot represents the mean expression within each sample and the size of each dot represents the fraction of cells expressing the specific genes in different samples. TCA tricarboxylic acid cycle. Source data are provided as a Source Data file.
