"strain: NEB 10-beta"	"characteristics_ch1.1"
"Reads mapped to reference using BWA versiopn 0.7.4 with default settings"	"data_processing.1"
"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 '-s reverse -a 10 -m union'."	"data_processing.2"
"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."	"data_processing.3"
"Genome_build: NC_010473.1"	"data_processing.4"
"Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units."	"data_processing.5"
"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."	"extract_protocol_ch1.1"
"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."	"extract_protocol_ch1.2"
"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. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into 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 and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Culture grown in 250 ml Erlenmeyer flask"	"source_name_ch1.1"
"Flask state 6 (IPTG+/aTc-/Ara+)"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: NEB 10-beta"	"characteristics_ch1.1"
"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. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into 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 and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Culture grown in 250 ml Erlenmeyer flask"	"source_name_ch1.1"