"strain: GLBRCE1"	"characteristics_ch1.1"
"medium: ACSH"	"characteristics_ch1.2"
"growth phase: Trans"	"characteristics_ch1.3"
"Probe signal intensities were preprocessed using robust multichip averaging (RMA) in the program ArrayStar (DNASTAR), and the resulting gene expression signals were quantile-normalized across all samples using the normalize.quantiles function in the Bioconductor package for R."	"data_processing.1"
"RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C"	"extract_protocol_ch1.1"
"E.coli ethanologen strain GLBRCE1 or GLBRCE1 lacking the plasmid-borne PET cassette (GLBRCE1_pBBR) was grown in AFEX corn stover hydrolysate (ACSH). Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH and cultures were diluted into ACSH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  One biological replicate was grown in each medium.  RNA samples were obtained at 3 time points, corresponding to mid-exponential (Exp), transitional (Trans), and stationary (Stat) growth phases."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli GLBRCE1"	"source_name_ch1.1"
"GLBRCE1_ACSH_Trans"	"title.1"
"Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C."	"treatment_protocol_ch1.1"
"strain: GLBRCE1"	"characteristics_ch1.1"
"medium: ACSH"	"characteristics_ch1.2"
"growth phase: Trans"	"characteristics_ch1.3"
"E.coli ethanologen strain GLBRCE1 or GLBRCE1 lacking the plasmid-borne PET cassette (GLBRCE1_pBBR) was grown in AFEX corn stover hydrolysate (ACSH). Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH and cultures were diluted into ACSH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  One biological replicate was grown in each medium.  RNA samples were obtained at 3 time points, corresponding to mid-exponential (Exp), transitional (Trans), and stationary (Stat) growth phases."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli GLBRCE1"	"source_name_ch1.1"
"Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C."	"treatment_protocol_ch1.1"