SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options [linebreak]-s reverse -a 10 -m union[linebreak]. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	Culture grown in 14 ml tube PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	strain: NEB 10-beta PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	Culture grown in 14 ml tube PGCGROWTHCONDITIONS
SRR5985593	GSE98890	GSM2757266	GPL18133	PMID_29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Thomas,Edward,Gorochowski PGCGROWTHCONDITIONS