Fig. 2: ProBac-seq analysis reveals distinct transcriptional states in B. subtilis.
From: Probe-based bacterial single-cell RNA sequencing predicts toxin regulation
a, Heatmap of marker gene expression (z-score of log-transformed values) from 2,784 individual B. subtilis cells organized into 10 clusters. b, UMAP two-dimensional representation of the 10 cell clusters reveals four highly distinct transcriptomic signatures. c, Top: single-cell expression of key marker genes for competence (comGE, clusters 6 and 8), sporulation (spoIIID, cluster 9) and arginine synthesis (argC, cluster 5) are highlighted on the UMAP (left to right). Cells within the highlighted cluster are boxed by dashed lines. Middle: volcano plots of genes expressed in at least 25% of cells in the corresponding clusters, with genes from the respective processes highlighted in green. P values correspond to two-sided Wilcoxon rank-sum test with Bonferroni correction. Lower: presence of each heterogeneous marker in the population as confirmed by fluorescent promoter-reporter constructs (PcomGE-YFP, PcotY-YFP and PargC-YFP, respectively). Representative images. A phase bright spore can be seen in the cotY-expressing cell. Scale bars, 1 µm. Microscope images were collected from at least ten fields with three biological replicates per reported strain to quantify phenotypes d, Of all comK regulon genes probed, 90% (45 out of 50) were significantly differentially upregulated in cell clusters 6 and 8 (Bonferroni-corrected P value ≤ 0.05 for each gene). See Supplementary Table 11 for information on comK regulon genes probed.
