SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Basecalling was done on the sequencers using the sequencer[linebreak]s Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with [linebreak]--nofw[linebreak] strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Genome_build: ASM584v2 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3[linebreak] ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	source_name	Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	treatment_protocol	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. PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	characteristics	strain: GLBRCE1 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	characteristics	medium: SynH PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	characteristics	growth phase: Stat1 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	source_name	Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	treatment_protocol	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. PGCGROWTHCONDITIONS
SRR1514616	GSE59397	GSM1436280	GPL14548-GPL18945	PMID_	SynH_Stat1_CBYN	Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (V)	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	contact_name	Robert,C,Landick PGCGROWTHCONDITIONS