Extended Data Fig. 3: Transcriptional differences between WT and Δxpk across 4 time points.
From: An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria
WT and Δxpk were grown under 12 h L/D cycle till OD730 reached 2. The samples were harvested 1 h after dark, at the end of dark, 1 h after light and at the end of light. Equal amount of RNA was extracted from both culture for RNA-seq analysis. a. Volcano plot between WT and Δxpk (n = 3 biological repeats, mean ± SEM). A few genes showed significant changes (red dots, p < 0.05). Their expressional fold change was less than 2 (x-axis, enlarged plot), except XPK and its downstream ACK. Thus, no global changes due to absence of XPK. The y axis represents FDR adjusted p-values, which are computed after first obtaining a two-sided Wald test p value by fitting expression data to a negative binominal Generalized Linear Model (GLM). b. The heat map showed the comparison of the 36 genes that appeared different in expression levels between WT and Δxpk (ANOVA-like statistical analysis by CLC) at 4 different time points. XPK was peaked at the end of light as an evening gene. However, the transcriptional differences are small as the z-values are ± 2.
