Supplementary Figure 4: Transcriptome data analysis.

(a) Venn diagrams of differentially expressed genes in MG1655 E. coli 1h post-induction. The set of significantly differentially expressed native genes (alpha < 0.05) was identified separately for each of three synthetic gene circuits comparing cells transformed with the synthetic circuits to cells transformed with the corresponding empty plasmids. Up-regulated and down-regulated genes for each sample are displayed in black and red, respectively; (b) List of top ten differentially expressed genes (black are up-regulated, red are down-regulated). Tables report the top ten differentially expressed genes for each construct and the associated regulatory sigma factors. Bold names indicate genes differentially expressed also at 15 min post-induction. Left columns show the differentially expressed genes that are shared among all 3 constructs; (c) Volcano plots. Volcano plots show genes that display large changes and are also statistically significant (DeSeq2, n=3). Symbol colors correspond to the constructs colors displayed in (a) with pSB1C3-Lux, pD864-LacZ and pSB1C3-H3 displayed in yellow, blue and red, respectively. (d) Transcription profiles of the dnaKJ, htpG, ibpAB and groSL regulons and the GFP monitor cassette from DH10B cells with induced synthetic construct pD864-LacZ and pSB1C3-H3. Top profiles are for strains containing only the empty plasmid 15 min post-induction, middle and bottom profiles are for strains containing synthetic constructs 15 and 60 min post-induction, respectively. Solid grey regions show average and transparent red regions span the min to max of transcription profiles generated from three biological replicates. Genetic designs below each profile are drawn using SBOLv notation.