antibody: Flag PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Cultures of Caulobacter (TLS1631-TLS1633) were grown at 30oC in PYE and supplemented with antibiotics, as necessary, at appropriate concentrations. To deplete wild-type non-tagged ParB, exponential-phase cells were washed off xylose and re-introduced to PYE+0.2% glucose for an additional 5 hours. After 4 hours, vanillate was added to induce the expression of flag-parB (WT) or flag-parB (G101S PGCGROWTHCONDITIONS
developmental stage: mixed population, exponential phase PGCGROWTHCONDITIONS
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli AB1157 PGCGROWTHCONDITIONS
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, reference genomes were first reconstructed in silico by inserting the nucleotide sequence of parS and apramycin antibiotic resistance cassette to the ybbD locus of E. coli MG1655 genome. Afterwards, Hiseq 2500 Illumina short reads were mapped back to these reconstructed reference genomes using Bowtie 1. Sequence coverage at each nucleotide position was also computed using BEDTools. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts. PGCGROWTHCONDITIONS
For analysis of IDAP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, sequencing reads were sorted to either being mapped to the upper DNA strand or to the lower strand of the reference genome, as suggested in the original IDAP-seq publication (Belitsky and Sonenshein, 2013). The number of 5’ end of reads that were mapped to the upper strand was counted for each nucleotide position along the Caulobacter genome using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -5 -strand + -ibam output.sorted.bam -g NA1000.fna > upper_strand_output.txt. To count the number of 5’ end of reads that were mapped to the lower strand, the following command was used instead: bedtools genomecov -d -5 -strand - -ibam output.sorted.bam -g NA1000.fna > lower_strand_output.txt. The IDAP-seq profile was then plotted using R. The sequence in between the summit of upper strand profile and that of the lower strand profile defines the minimal parS sequence required for binding to ParB. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
Genome_build: NC_011916.1 PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS scrambled site 3 pUTC18::parB (G101S) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS scrambled site 3 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 1 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 2 pUTC18::parB (G101S) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 2 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 3 pUTC18::parB (G101S) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 3 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 4 pUTC18::parB (G101S) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 4 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 5 pUTC18::parB (G101S) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 5 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 6 pUTC18::parB (WT) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 7 pUTC18::parB (G101S) PGCGROWTHCONDITIONS
genotype: AB1157 ybbD::parS site 7 pUTC18::parB (WT) PGCGROWTHCONDITIONS
Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage for each nucleotide position was computed using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, the ratio between the number of reads of libraries generated from pMCS1-Tn5-ME-R6Kγ-kanR-ME or pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME were calculated. Results were binned over 1 kb and represented as a log10 scale. PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1637_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1638_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1639_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1640_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1641_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1642_anti_FLAG PGCGROWTHCONDITIONS
LELAb_ChIP_seq_TLS1643_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1644_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1645_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1646_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1647_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1648_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1649_anti_FLAG PGCGROWTHCONDITIONS
LELab_ChIP_seq_TLS1650_anti_FLAG PGCGROWTHCONDITIONS
None PGCGROWTHCONDITIONS
Standard library construction for Illumina Hiseq2500 sequencing platform PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage) PGCGROWTHCONDITIONS
T18-ParB (G101S) were produced by addition of 0.5mM IPTG for an hour before formadehyde to 1% (final concentration ) was added to fix cells for ChIP-seq PGCGROWTHCONDITIONS
T18-ParB (WT) were produced by addition of 0.5mM IPTG for an hour before formadehyde to 1% (final concentration ) was added to fix cells for ChIP-seq PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.8.3, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli CMA540(MG1693 ∆hfq::cat) PGCGROWTHCONDITIONS
E. coli MG1693 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 1.1.2, parameters for samples 1-2: -v 2 --best --strata -m 1 PGCGROWTHCONDITIONS
growth phase: Exponential PGCGROWTHCONDITIONS
Hfq mut exp mRNA PGCGROWTHCONDITIONS
Hfq mut exp RPF PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counting using bedtools, version 2.17.0, parameter: -s, the middle nucleotide of each read was taken PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
strain: CMA540(MG1693 delta_hfq::cat) PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Strains were grown in LB medium (Difco) supplemented with thymine (50 µg PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts were normalized by the length of the unique CDS per kilobase (RPKM) and the total mapped reads per million (RPM) PGCGROWTHCONDITIONS
Total RNA was extracted using TRI Reagent (Sigma Aldrich), enriched by depleting small RNAs with GeneJET Purification Kit (Fermentas) and rRNA with MICROBExpres Bacterial mRNA Enrichment Kit (Ambion) and fragmented in alkaline solution (2 mM EDTA and 100 mM Na2CO3 pH 9.2 for 40 min at 95°C) to fragments with size of 24-35 nts. For RPFS, cells were lysed by freeze-rupturing (Retch Mill) and 100 A260 units of ribosome-bound mRNA fraction were directly used for polysomal analysis or subjected to nucleolytic digestion with 10 units PGCGROWTHCONDITIONS
WT exp mRNA PGCGROWTHCONDITIONS
WT exp RPF PGCGROWTHCONDITIONS
All cultures were grown at 37C in well-mixed minimal media modified with M63 (mM63: pH 7.0, 62 mM K2HPO4, 39 mM KH2PO4, 15 mM ammonium sulfate, 1.8 µM FeSO4-7H2O, 15 µM thiamine hydrochloride, 0.2 mM MgSO4-7H2O and 22 mM glucose). One amino acid, Ile or Leu, was added to the monoculture medium when appropriate. Prior to coculturing, at both the initial inoculation and transfer, we washed the E. coli cells with fresh mM63 without amino acids to exclude the carry-over of supplements from the pre-culture. For coculture samples, we used cell culture inserts with a pore size of 0.45 µm at a density of 10^8 PGCGROWTHCONDITIONS
Ancestral I- cells at amino acid starvation in monoculture PGCGROWTHCONDITIONS
Ancestral I- cells at log phase in monoculture PGCGROWTHCONDITIONS
Ancestral I- cells in coculture PGCGROWTHCONDITIONS
Ancestral I- cells in coculture, a biological replicate PGCGROWTHCONDITIONS
Ancestral L- cells at amino acid starvation in monoculture PGCGROWTHCONDITIONS
Ancestral L- cells at log phase in monoculture PGCGROWTHCONDITIONS
Ancestral L- cells at log phase in monoculture, a technical replicate PGCGROWTHCONDITIONS
Ancestral L- cells in coculture PGCGROWTHCONDITIONS
Ancestral L- cells in coculture, a biological replicate PGCGROWTHCONDITIONS
cell type: Ancestral I- cells PGCGROWTHCONDITIONS
cell type: Ancestral L- cells PGCGROWTHCONDITIONS
cell type: Evolved I- cells PGCGROWTHCONDITIONS
cell type: Evolved L- cells PGCGROWTHCONDITIONS
cell type: Original prototroph DH1 cells PGCGROWTHCONDITIONS
culture type: coculture PGCGROWTHCONDITIONS
culture type: monoculture PGCGROWTHCONDITIONS
DH1-log PGCGROWTHCONDITIONS
DH1-log-tr PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Evolved I- cells at amino acid starvation in monoculture PGCGROWTHCONDITIONS
Evolved I- cells at log phase in monoculture PGCGROWTHCONDITIONS
Evolved I- cells in coculture PGCGROWTHCONDITIONS
Evolved I- cells in coculture, a biological replicate PGCGROWTHCONDITIONS
Evolved L- cells at amino acid starvation in monoculture PGCGROWTHCONDITIONS
Evolved L- cells at log phase in monoculture PGCGROWTHCONDITIONS
Evolved L- cells at log phase in monoculture, a technical replicate PGCGROWTHCONDITIONS
Evolved L- cells in coculture PGCGROWTHCONDITIONS
Evolved L- cells in coculture, a biological replicate PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth type: amino acid starvation PGCGROWTHCONDITIONS
growth type: log phase PGCGROWTHCONDITIONS
IA-co1 PGCGROWTHCONDITIONS
IA-co2 PGCGROWTHCONDITIONS
IA-log PGCGROWTHCONDITIONS
IA-starve PGCGROWTHCONDITIONS
IE-co1 PGCGROWTHCONDITIONS
IE-co2 PGCGROWTHCONDITIONS
IE-log PGCGROWTHCONDITIONS
IE-starve PGCGROWTHCONDITIONS
LA-co1 PGCGROWTHCONDITIONS
LA-co2 PGCGROWTHCONDITIONS
LA-log PGCGROWTHCONDITIONS
LA-log-tr PGCGROWTHCONDITIONS
LA-starve PGCGROWTHCONDITIONS
LE-co1 PGCGROWTHCONDITIONS
LE-co2 PGCGROWTHCONDITIONS
LE-log PGCGROWTHCONDITIONS
LE-log-tr PGCGROWTHCONDITIONS
LE-starve PGCGROWTHCONDITIONS
Metabolome data for these cultures are also provided in the supplementary file \Ecoli_co_results.xlsx\, just for information. PGCGROWTHCONDITIONS
Microarray data were processed using a custom R software for the finite hybridisation (FH) model (Ono et al., 2008, Bioinformatics 24, p1278). PGCGROWTHCONDITIONS
Original prototroph DH1 cells at log phase in monoculture PGCGROWTHCONDITIONS
Original prototroph DH1 cells at log phase in monoculture, a technical replicate PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
substrain: DH1 PGCGROWTHCONDITIONS
The cell cultures were interrupted by placing them directly into a cold phenol-ethanol solution (0.1g-phenol PGCGROWTHCONDITIONS
The processed gene expression data in log10 scale are provided in the supplementary file \Ecoli_co_results.xlsx\. PGCGROWTHCONDITIONS
The total RNA was extracted using an RNeasy kit, Qiagen, in accordance with the manufacturer's instructions. PGCGROWTHCONDITIONS
After normalization, the read counts were estimated in the running windows of 35 bp, and the ratios R between values obtained for experimental and control libraries were calculated. Peaks were localized requiring R≥1.5 for at least 50% positions of at least 60 bp genomic region in length. PGCGROWTHCONDITIONS
antibody: Anti-Dps antibodies PGCGROWTHCONDITIONS
antibody: rabbit pre-immune IgG PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Bacterial cells were grown aerobically in M9 medium supplemented with 0.2% glucose and 5% LB at 37°C under constant shaking (~120 rpm) in a water bath and harvested at OD ~0.6. PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq experiments were performed in duplicate using similar growth condition and protocols for chromatin immunoprecipitation. The first experiment was done in the Centre for Genomic Regulation (CRG, Barcelona, Spain), while the second one in the Immanuel Kant Baltic Federal University (Kaliningrad, Russia). In both cases, bacterial cells were grown aerobically at 37°C until OD600~0.6 were treated with formaldehyde (final concentration of 1%, 20 min incubation). Cross-linking was stopped with glycine (final concentration of 450 mM). After 5 minutes of incubation the cells were pelleted by centrifugation at 14,000 rpm for 15 minutes (+4°C), washed twice with 5 ml of PBS and resuspended in 1.3 ml of ice-cold immunoprecipitation buffer prepared from 50 ml of buffer containing 100 mM NaCl, 50 mM Tris-HCl (pH 8.1), 5 mM EDTA, 0.2% NaN3, 0.5% SDS, and 25 ml of buffer containing 100 mM Tris-HCl (pH 8.6); 100 mM NaCl; 5 mM EDTA; 0,2% NaN3, 5% Triton-X-100. Then phenylmethylsulfonyl fluoride (final concentration of 1 mM) or 20 μl of Protease Inhibitor Cocktail (PIC, Sigma) for the first and the second experiment, respectively, were added followed by incubation for 30 min at +4°C. PGCGROWTHCONDITIONS
ChIP-seq libraries were prepared from 5-10 ng of the DNA samples with the NebNext® Ultra™ DNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) following the manufacturer’s instructions. For the final amplification of the library 15 PCR cycles were used. Size distribution and concentration of the amplicons was checked on the Bioanalyzer 2100 (Agilent, USA). In the first experiment, the maximum was at about 300 bp, and ChIP libraries were sequenced using 50 nt single-end read protocol on the Illumina HiSeq system (Illumina, USA) of the Genomics Facility in the Centre for Genomic Regulation (Barcelona). In the second experiment, the maximum was at about 450 bp, and samples were sequenced using standard paired-end 2*150 nt protocol on the MiSeq system (Illumina, USA) in the Immanuel Kant Baltic Federal University (Kaliningrad). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Exp 1_control PGCGROWTHCONDITIONS
Exp 1_IP sample PGCGROWTHCONDITIONS
Exp 2_control PGCGROWTHCONDITIONS
Exp 2_IP sample PGCGROWTHCONDITIONS
For immunoprecipitation, 800 μl of collected chromatin (~1000 μg of protein) were incubated on a rotating wheel over night at 4°C with 10 μg of either rabbit anti-Dps antibodies (experimental sample) or rabbit pre-immune IgG (negative control). Next day 30 μl of Ultra Link Protein A PGCGROWTHCONDITIONS
Genome_build: E. coli K-12 MG1655 (U00096.3) PGCGROWTHCONDITIONS
growth stage: log-phase PGCGROWTHCONDITIONS
medium: M9 medium supplemented with 0.2% glucose and 5% LB PGCGROWTHCONDITIONS
ngs platform: Illumina HiSeq PGCGROWTHCONDITIONS
ngs platform: Illumina MiSeq PGCGROWTHCONDITIONS
Only ideal correspondence of sequence reads to the genome in both cases was permitted. The profiles obtained for experimental and control samples were normalized by the scaling method initially offered by Affymetrix for microarray data analysis and later implemented in several other approaches. This method assumes unaffected protein occupancy at most genomic positions and quantifies the scaling factor on the basis of corrected mean values obtained after removal of 2% signals with highest and lowest intensities from both control and experimental sets. PGCGROWTHCONDITIONS
Raw data were quality filtered on the Galaxy server (Filter by Quality tool, Q≥20) providing 99% probability of correct sequencing for all nucleotides in each read. As a result, the sets contain 31,656,551 and 45,396,252 sequences in the control and immunoprecipitated samples of the first experiment, and, respectively, 7,493,528 and 8,214,737 reads for the second experiment. PGCGROWTHCONDITIONS
sequencing mode: 50 nt single-end read protocol PGCGROWTHCONDITIONS
sequencing mode: paired-end 2*150 nt protocol PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data include read pileups obtained in two ChIP-seq experiments by two different approaches (files 1-4), the set of regions bound by Dps in both experiments (file 5) and the set of regions unbound by Dps in both experiments (file 6). All processed data are provided as tab-delimited .txt files. PGCGROWTHCONDITIONS
To apply the second approach variable in length reads from Illumina MiSeq were first trimmed from both sides to obtain a set of standard 50 nt sequences taken from the middle of longer reads. Reads shorter than 50 nt were discarded. Then, all four sets from both experiments were aligned to the genome using the Matcher program (available at: http: PGCGROWTHCONDITIONS
Two different approaches were used to align sequence reads to the genome of E. coli K-12 MG1655 (U00096.3). First, quality controlled reads were mapped using the CLC Genomics Workbench version 7.5.1 (CLC GW, Bio-Qiagen, Aarhus, Denmark) with either default settings for the length and similarity fractions (0.5 and 0.8, respectively, see supplemental Table 2 of the paper) or with the most stringent criteria (1.0 and 1.0, respectively, deposited). Reads with sequences aligned to multiple genomic regions were ignored. PGCGROWTHCONDITIONS
Agilent Scan Control Software V.8.5 at a resolution of 3μm. The data was extracted using Agilent Feature extraction software V 10.10 PGCGROWTHCONDITIONS
azide treated PGCGROWTHCONDITIONS
Cells were subcultured from overnight cultures into 20 ml of LB media PGCGROWTHCONDITIONS
cultures were split into two 10 ml cultures. One half was treated with 2 mM NaN3 for 10 minutes and the other half was left untreated PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
growth media: LB PGCGROWTHCONDITIONS
od: 0.8 PGCGROWTHCONDITIONS
Sample 1 PGCGROWTHCONDITIONS
Sample 2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Total RNA using Qiagen RNeasy kit PGCGROWTHCONDITIONS
treatment: 2 mM NaN3 for 10 minutes PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
untreated PGCGROWTHCONDITIONS
Adaptive threshold (quantitation method) uses the parameters of the spot diameter and background inner and outer dimensions to create a spot mask and background mask, then refines the mask on a pixel-by-pixel basis. Total (normalization method), uses the intensity of each spot in relation to all spots. PGCGROWTHCONDITIONS
E. coli, glucose limitation, 110 min after depletion of extracellular acetate PGCGROWTHCONDITIONS
E. coli, glucose limitation, 170 min after depletion of extracellular acetate PGCGROWTHCONDITIONS
E. coli, glucose limitation, 230 min after depletion of extracellular acetate PGCGROWTHCONDITIONS
E. coli, glucose limitation, 30 min after depletion of extracellular acetate PGCGROWTHCONDITIONS
E. coli, glucose limitation, 350 min after depletion of extracellular acetate PGCGROWTHCONDITIONS
E. coli, glucose limitation, 50 min after depletion of extracellular acetate PGCGROWTHCONDITIONS
E. coli, glucose limitation, acetate concentration ≤ 0.35 gL-1 PGCGROWTHCONDITIONS
E. coli, glucose limitation (glucose concentration < 0.05 gL-1) PGCGROWTHCONDITIONS
E. coli, glucose limitation (glucose concentration < 0.05 gL-1), fed-batch PGCGROWTHCONDITIONS
E. coli K12 (W3110), fed-batch PGCGROWTHCONDITIONS
E.coli_RviaT1_SR1 PGCGROWTHCONDITIONS
E.coli_RviaT1_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT1_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT2_SR1 PGCGROWTHCONDITIONS
E.coli_RviaT2_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT2_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT3_SR1 PGCGROWTHCONDITIONS
E.coli_RviaT3_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT3_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT4_SR1 PGCGROWTHCONDITIONS
E.coli_RviaT4_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT4_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT5_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT5_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT6_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT6_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT7_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT7_SR3 PGCGROWTHCONDITIONS
E.coli_RviaT8_SR2 PGCGROWTHCONDITIONS
E.coli_RviaT8_SR3 PGCGROWTHCONDITIONS
E.coli_T1viaR_SR1 PGCGROWTHCONDITIONS
E.coli_T1viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T1viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T2viaR_SR1 PGCGROWTHCONDITIONS
E.coli_T2viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T2viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T3viaR_SR1 PGCGROWTHCONDITIONS
E.coli_T3viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T3viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T4viaR_SR1 PGCGROWTHCONDITIONS
E.coli_T4viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T4viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T5viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T5viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T6viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T6viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T7viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T7viaR_SR3 PGCGROWTHCONDITIONS
E.coli_T8viaR_SR2 PGCGROWTHCONDITIONS
E.coli_T8viaR_SR3 PGCGROWTHCONDITIONS
E. coli, unlimited growth (batch) PGCGROWTHCONDITIONS
E. coli, unlimited growth (batch)  PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. W3110 PGCGROWTHCONDITIONS
Raw data were created by analyzing 16-bit tiff files with the Scan Array Express imaging software (microarray analysis system, version 3.0.0.0016, PerkinElmer, Massachusetts, USA; adaptive treshold method, total normalization method). PGCGROWTHCONDITIONS
The cell samples were collected directly into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to avoid RNA degradation. The samples were centrifuged according to the manufacturer’s protocol and frozen at - 80 °C until RNA isolation. PGCGROWTHCONDITIONS
The culture medium samples were withdrawn with a capillary sampling probe as developed by Theobald et al. (1997), however, without using membrane-covered glass tubes. PGCGROWTHCONDITIONS
The fed-batch cultivations were carried out with the bacterial strain E. coli K-12 W3110 (DSM 5911, German Collection of Microorganisms and Cell Cultures) in a 30-l bioreactor (Bioengineering AG, Wald, Switzerland). Minimal medium supplemented with glucose as the carbon source was used. The batch medium (batch volume VR,0 =17 l) consisted of 8.8 g l−1 glucose•H2O, 2.0 g l−1 Na2SO4•10H2O, 2.68 g l−1 (NH4)2SO4, 1.0 g l−1 NH4Cl, 14.6 g l−1 K2HPO4, 4.02 g l−1 NaH2PO4•2H2O, 0.01 g l−1 thiamine HCl; 0.3mM CaCl2•2H2O, 2mM MgSO4•7H2O; 3ml l−1 of trace element solution (TES: 16.7 g l−1 FeCl3•6H2O, 20.1 g l−1 PGCGROWTHCONDITIONS
Theobald, U., Mailinger,W., Baltes, M., Rizzi, M., Reuss, M., 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 1. Experimental observations. Biotechnol. Bioeng. 55, 305–316. PGCGROWTHCONDITIONS
The VALUE data are normalized log2(test PGCGROWTHCONDITIONS
Total RNA from 8.1*10exp9 cells was isolated using the RNeasy Kit (Qiagen) according to the manufacturer’s protocol. On-column DNase digestion was performed (RNase free DNase set, Qiagen). RNA concentration and quality were assessed photometrically (Nanodrop ND 1000, NanoDrop Technologies, Inc., Delaware, USA), by formaldehyde gel electrophoresis and bioanalyzer analysis (RNA 6000 Nano LabChip Kit, Agilent Bioanalyzer 2100, Agilent Technologies, California, USA). Only RNA with 260 nm  PGCGROWTHCONDITIONS
An RNeasy minikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0052 (in DMSO) PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0053 (in DMSO) PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0054 (in DMSO) PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0055 (in DMSO) PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 MEM-HEPES + DMSO PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown at 37 degrees C to OD 0.7 in MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2. PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown at 37 degrees C to OD 0.7 in MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2 and and equivalent volume of DMSO. PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0052 PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0053 PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0054 PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0055 PGCGROWTHCONDITIONS
Escherichia coli O157 TUV93-0 was grown in the presence of DMSO PGCGROWTHCONDITIONS
inhibitor: 20uM ME0052 PGCGROWTHCONDITIONS
inhibitor: 20uM ME0053 PGCGROWTHCONDITIONS
inhibitor: 20uM ME0054 PGCGROWTHCONDITIONS
inhibitor: 20uM ME0055 PGCGROWTHCONDITIONS
LOWESS normalised data that represents the average of the three replicate experiments PGCGROWTHCONDITIONS
ME0052 PGCGROWTHCONDITIONS
ME0053 PGCGROWTHCONDITIONS
ME0054 PGCGROWTHCONDITIONS
ME0055 PGCGROWTHCONDITIONS
media: MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2 PGCGROWTHCONDITIONS
no inhibitor: equivalent volume of DMSO added PGCGROWTHCONDITIONS
od: 0.7 PGCGROWTHCONDITIONS
strain: O157:H7 EHEC TUV93-0 PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C, rep1 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C, rep2 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C, rep 3 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C, rep 4 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.025mM CspA protein PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.05mM CspA protein PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep1 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep 2 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep 3 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep 4 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 37°C PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 37°C, rep1 PGCGROWTHCONDITIONS
DMS-MaPSeq of purified cspA mRNA at 37°C, rep 2 PGCGROWTHCONDITIONS
DMS-seq 30 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
DMS-seq 6 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells PGCGROWTHCONDITIONS
DMS-seq 8 hr after shift to 10°C in ∆cspBG cells PGCGROWTHCONDITIONS
DMS-seq 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
DMS-seq of purified mRNA in vitro at 10°C, rep1 PGCGROWTHCONDITIONS
DMS-seq of purified mRNA in vitro at 10°C, rep2 PGCGROWTHCONDITIONS
DMS-seq of WT cells after kasugamycin treatment at 10°C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For DMS-MaPSeq, reads were aligned to the 5’UTR of cspA using bowtie2 and an alignment seed of 12nt.  Low sequence quality bases (Q score < 20%) and missing bases due to truncated reads were set to question marks. Reads that consisted of more than 20% question marks were filtered out. Only mutations that agreed between the forward and the reverse read were considered true mutations. Mutation rate per base was calculated as number of reads with a mutation at the base divided by total number of reads covering the base. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
MG1655 ∆cspABCEG PGCGROWTHCONDITIONS
MG1655 ∆cspABEG PGCGROWTHCONDITIONS
MG1655 ∆cspBG PGCGROWTHCONDITIONS
MG1655 ∆rnr PGCGROWTHCONDITIONS
molecule subtype: DMS-modified mRNA PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 10 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq 2 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq 30 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq 3 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq 6 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells PGCGROWTHCONDITIONS
mRNA-seq 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
mRNA-seq at 37°C in ∆cspABCEG cells PGCGROWTHCONDITIONS
mRNA-seq at 37°C in WT cells_1 PGCGROWTHCONDITIONS
mRNA-seq at 37°C in WT cells_2 PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
Ribosome profiling 10 min after shift to 10°C in WT cells_1 PGCGROWTHCONDITIONS
Ribosome profiling 10 min after shift to 10°C in WT cells_2 PGCGROWTHCONDITIONS
Ribosome profiling 15 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 2 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 30 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 3 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 5 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 6 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells PGCGROWTHCONDITIONS
Ribosome profiling 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Ribosome profiling at 37°C in ∆cspABCEG cells PGCGROWTHCONDITIONS
Ribosome profiling at 37°C in WT cells_1 PGCGROWTHCONDITIONS
Ribosome profiling at 37°C in WT cells_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Txt files are processed data for DMS-MaPseq with two columns: first column containing chromosome positions (relative to transcription start site (1) of cspA) and second column containing the mutation rate. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 20 min after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Total RNA-seq 20 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Total RNA-seq 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Total RNA-seq 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
treatment: 0.025mM CspA protein PGCGROWTHCONDITIONS
treatment: 0.05mM CspA protein PGCGROWTHCONDITIONS
treatment: 0.1mM CspA protein PGCGROWTHCONDITIONS
treatment: After 10 mg PGCGROWTHCONDITIONS
treatment: After 250 µg PGCGROWTHCONDITIONS
treatment: Before rifampicin treatment PGCGROWTHCONDITIONS
treatment: NA PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
Bicyclomycin (BCM, gift of Schering-Plough Animal Health) was added to the culture at the indicated dose for 20 minutes. Culture was added to 2 volumes of RNAprotect Bacterial Reagent (QIAGEN). PGCGROWTHCONDITIONS
Coli-MDS42_bcm-100mcg PGCGROWTHCONDITIONS
Coli-MDS42_del-nusA_rep1 PGCGROWTHCONDITIONS
Coli-MDS42_del-nusA_rep2 PGCGROWTHCONDITIONS
Coli-MDS42_del-nusG_rep1 PGCGROWTHCONDITIONS
Coli-MDS42_del-nusG_rep2 PGCGROWTHCONDITIONS
Coli-MDS42_no-drug_rep1 PGCGROWTHCONDITIONS
Coli-MDS42_no-drug_rep2 PGCGROWTHCONDITIONS
Coli-MG1655_bcm-100mcg PGCGROWTHCONDITIONS
Coli-MG1655_bcm-10mcg PGCGROWTHCONDITIONS
Coli-MG1655_bcm-25mcg PGCGROWTHCONDITIONS
Coli-MG1655_no-drug_rep1 PGCGROWTHCONDITIONS
Coli-MG1655_no-drug_rep2 PGCGROWTHCONDITIONS
Coli-O157H7_bcm-100mcg PGCGROWTHCONDITIONS
Coli-O157H7_no-drug_rep1 PGCGROWTHCONDITIONS
Coli-O157H7_no-drug_rep2 PGCGROWTHCONDITIONS
Culture conditions: 37 C with shaking at 220 RPM PGCGROWTHCONDITIONS
Drug: bicyclomycin PGCGROWTHCONDITIONS
Drug: none PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction: Rneasy PGCGROWTHCONDITIONS
Extraction: TRI Reagent PGCGROWTHCONDITIONS
Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the PLIER algorithm in the Affymetrix Expression Console. No further adjustments were made to the data in the table. PGCGROWTHCONDITIONS
Growth medium: MOPS minimal, 0.4% glucose, 0.5% casamino acids PGCGROWTHCONDITIONS
Growth phase: exponential PGCGROWTHCONDITIONS
Growth phase: OD600=0.3 PGCGROWTHCONDITIONS
Isolate: EDL933 PGCGROWTHCONDITIONS
Isolate: MDS42 PGCGROWTHCONDITIONS
Isolate: MG1655 PGCGROWTHCONDITIONS
K12 strain MG1655, 100 mcg PGCGROWTHCONDITIONS
K12 strain MG1655, 10 mcg PGCGROWTHCONDITIONS
K12 strain MG1655, 25 mcg PGCGROWTHCONDITIONS
K12 strain MG1655, control sample, exponential phase PGCGROWTHCONDITIONS
O157:H7 strain EDL933, 100 mcg PGCGROWTHCONDITIONS
O157:H7 strain EDL933, control sample, exponential phase PGCGROWTHCONDITIONS
Overnight culture in LB medium was innoculated from a single colony. The overnight culture was diluted 1 PGCGROWTHCONDITIONS
Reduced genome strain MDS42, 100 mcg PGCGROWTHCONDITIONS
Reduced genome strain MDS42, control sample, exponential phase PGCGROWTHCONDITIONS
Reduced genome strain MDS42, deletion of nusA gene, OD600=0.3 PGCGROWTHCONDITIONS
Reduced genome strain MDS42, deletion of nusG gene, OD600=0.3, overnight culture PGCGROWTHCONDITIONS
Strain: K-12 PGCGROWTHCONDITIONS
Strain: K-12 reduced genome PGCGROWTHCONDITIONS
Strain: O157:H7 PGCGROWTHCONDITIONS
TRI Reagent (Sigma) or Rneasy (QIAGEN) according to manufacturer's protocol. No Rnase treatment. PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}nusG PGCGROWTHCONDITIONS
genotype: {delta}rho PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
∆nusG UvsW_replicate1 PGCGROWTHCONDITIONS
∆nusG UvsW_replicate2 PGCGROWTHCONDITIONS
∆nusG UvsW_replicate3 PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
∆rho UvsW_replicate1 PGCGROWTHCONDITIONS
∆rho UvsW_replicate2 PGCGROWTHCONDITIONS
∆rho UvsW_replicate3 PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13507 PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
substrain: GJ13531 PGCGROWTHCONDITIONS
substrain: GJ13533 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531 PGCGROWTHCONDITIONS
WT glucose_replicate1 PGCGROWTHCONDITIONS
WT glucose_replicate2 PGCGROWTHCONDITIONS
WT glucose_replicate3 PGCGROWTHCONDITIONS
WT_glycerol_replicate1 PGCGROWTHCONDITIONS
WT_glycerol_replicate2 PGCGROWTHCONDITIONS
WT_glycerol_replicate3 PGCGROWTHCONDITIONS
WT UvsW_replicate1 PGCGROWTHCONDITIONS
WT UvsW_replicate2 PGCGROWTHCONDITIONS
WT UvsW_replicate3 PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crpfis.rep1.ee PGCGROWTHCONDITIONS
crpfis.rep1.me PGCGROWTHCONDITIONS
crpfis.rep2.ee PGCGROWTHCONDITIONS
crpfis.rep2.me PGCGROWTHCONDITIONS
crp.rep1.ee PGCGROWTHCONDITIONS
crp.rep1.me PGCGROWTHCONDITIONS
crp.rep2.ee PGCGROWTHCONDITIONS
crp.rep2.me PGCGROWTHCONDITIONS
cya.rep1.ee PGCGROWTHCONDITIONS
cya.rep1.me PGCGROWTHCONDITIONS
cya.rep2.ee PGCGROWTHCONDITIONS
cya.rep2.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
fis.rep1.ee PGCGROWTHCONDITIONS
fis.rep1.me PGCGROWTHCONDITIONS
fis.rep2.ee PGCGROWTHCONDITIONS
fis.rep2.me PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crpfis mutant background PGCGROWTHCONDITIONS
genotype: crp mutant background PGCGROWTHCONDITIONS
genotype: cya mutant background PGCGROWTHCONDITIONS
genotype: fis mutant background PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1655 PGCGROWTHCONDITIONS
srain: K12 MG1656 PGCGROWTHCONDITIONS
srain: K12 MG1657 PGCGROWTHCONDITIONS
srain: K12 MG1658 PGCGROWTHCONDITIONS
srain: K12 MG1659 PGCGROWTHCONDITIONS
srain: K12 MG1660 PGCGROWTHCONDITIONS
srain: K12 MG1661 PGCGROWTHCONDITIONS
srain: K12 MG1662 PGCGROWTHCONDITIONS
srain: K12 MG1663 PGCGROWTHCONDITIONS
srain: K12 MG1664 PGCGROWTHCONDITIONS
srain: K12 MG1665 PGCGROWTHCONDITIONS
srain: K12 MG1666 PGCGROWTHCONDITIONS
srain: K12 MG1667 PGCGROWTHCONDITIONS
srain: K12 MG1668 PGCGROWTHCONDITIONS
srain: K12 MG1669 PGCGROWTHCONDITIONS
srain: K12 MG1670 PGCGROWTHCONDITIONS
srain: K12 MG1671 PGCGROWTHCONDITIONS
srain: K12 MG1672 PGCGROWTHCONDITIONS
srain: K12 MG1673 PGCGROWTHCONDITIONS
srain: K12 MG1674 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
wt.rep1.ee PGCGROWTHCONDITIONS
wt.rep1.me PGCGROWTHCONDITIONS
wt.rep2.ee PGCGROWTHCONDITIONS
wt.rep2.me PGCGROWTHCONDITIONS
cell pellets PGCGROWTHCONDITIONS
E. coli 042 WT PGCGROWTHCONDITIONS
E. coli hhahha2 PGCGROWTHCONDITIONS
E. coli hns PGCGROWTHCONDITIONS
E. coli hns2 PGCGROWTHCONDITIONS
E. coli hnshns2 PGCGROWTHCONDITIONS
Escherichia coli 042 PGCGROWTHCONDITIONS
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr PGCGROWTHCONDITIONS
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence (NC_017626.1) PGCGROWTHCONDITIONS
genotype: mutant hhahha2 PGCGROWTHCONDITIONS
genotype: mutant hhs PGCGROWTHCONDITIONS
genotype: mutant hns2 PGCGROWTHCONDITIONS
genotype: mutant hnshns2 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina. PGCGROWTHCONDITIONS
LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters. PGCGROWTHCONDITIONS
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). PGCGROWTHCONDITIONS
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. PGCGROWTHCONDITIONS
E.coli_∆ompR pH 5.6 A PGCGROWTHCONDITIONS
E.coli_∆ompR pH 5.6 B PGCGROWTHCONDITIONS
E.coli_∆ompR pH 5.6 C PGCGROWTHCONDITIONS
E.coli_∆ompR pH 7.2+15% sucrose A PGCGROWTHCONDITIONS
E.coli_∆ompR pH 7.2+15% sucrose B PGCGROWTHCONDITIONS
E. coli strains was grown in MgM media at pH 5.6, 7.2 and 7.2 with 15% (w PGCGROWTHCONDITIONS
E.coli_WT pH 5.6 A PGCGROWTHCONDITIONS
E.coli_WT pH 5.6 B PGCGROWTHCONDITIONS
E.coli_WT pH 5.6 C PGCGROWTHCONDITIONS
E.coli_WT pH 7.2+15% sucrose A PGCGROWTHCONDITIONS
E.coli_WT pH 7.2+15% sucrose B PGCGROWTHCONDITIONS
E.coli_WT pH 7.2+15% sucrose C PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype: delta_ompR PGCGROWTHCONDITIONS
genotype: Wildtype PGCGROWTHCONDITIONS
∆ompR pH 5.6 A PGCGROWTHCONDITIONS
∆ompR pH 5.6 B PGCGROWTHCONDITIONS
∆ompR pH 5.6 C PGCGROWTHCONDITIONS
∆ompR pH 7.2+15% sucrose A PGCGROWTHCONDITIONS
∆ompR pH 7.2+15% sucrose B PGCGROWTHCONDITIONS
ph: 5.6 PGCGROWTHCONDITIONS
ph: 7.2 PGCGROWTHCONDITIONS
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The data analysis is done using a microarray specialized analysis software, Genespring GX. In this experiment, the microarray type used is a slide having 8 arrays with 60 thousand features per array. The exact number of features in the each array, inclusive of control probes, is 10,751 features. The microarray has a specific Agilent identifier called an AMADID which is used to identify what kind of array is being used; in this experiment the AMADID used is the design ID 020097. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
sucrose status: no sucrose PGCGROWTHCONDITIONS
sucrose status: with 15% sucrose PGCGROWTHCONDITIONS
Supplementary files contain the following: Raw Signal Values: The term “raw” signal values refer to the linear data after thresholding and summarization Summarization is performed by computing the geometric mean. Raw data filtered on Expression (20.0 - 343943.344)• Normalized Signal Values: ``Normalized'' value is the value generated after log transformation and normalization (Shift to 75 percentile) and baseline transformation. PGCGROWTHCONDITIONS
The total RNA was isolated using an RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
WT pH 5.6 A PGCGROWTHCONDITIONS
WT pH 5.6 B PGCGROWTHCONDITIONS
WT pH 5.6 C PGCGROWTHCONDITIONS
WT pH 7.2+15% sucrose A PGCGROWTHCONDITIONS
WT pH 7.2+15% sucrose B PGCGROWTHCONDITIONS
WT pH 7.2+15% sucrose C PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B10 DH10BGFP_pSB1C3_2 PGCGROWTHCONDITIONS
B17 MG1655GFP_pSB1C3_2 PGCGROWTHCONDITIONS
B22 MG1655GFP_pSB1C3_H3_2 PGCGROWTHCONDITIONS
B26 MG1655GFP_Lux_2 PGCGROWTHCONDITIONS
B3 DH10BGFP_pSB1C3_2 PGCGROWTHCONDITIONS
B4 DH10BGFP_pLys_2 PGCGROWTHCONDITIONS
B7 DH10BGFP_pD864_2 PGCGROWTHCONDITIONS
B9 DH10BGFP_pLys_M1_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G21 MG1655GFP_pD864_3 PGCGROWTHCONDITIONS
G23 MG1655GFP_pLys_M1_3 PGCGROWTHCONDITIONS
G28 MG1655GFP_pD864_3 PGCGROWTHCONDITIONS
G29 DH10BGFP_None_3 PGCGROWTHCONDITIONS
G5 DH10BGFP_Lux_3 PGCGROWTHCONDITIONS
G6 DH10BGFP_pD864_LacZ_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: None PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
R11 DH10BGFP_pLys_1 PGCGROWTHCONDITIONS
R16 MG1655GFP_pLys_M1_1 PGCGROWTHCONDITIONS
R19 MG1655GFP_Lux_1 PGCGROWTHCONDITIONS
R26 MG1655GFP_Lux_1 PGCGROWTHCONDITIONS
R27 MG1655GFP_pD864_LacZ_1 PGCGROWTHCONDITIONS
R29 DH10BGFP_None_1 PGCGROWTHCONDITIONS
R2 DH10BGFP_pLys_M1_1 PGCGROWTHCONDITIONS
R3 DH10BGFP_pSB1C3_1 PGCGROWTHCONDITIONS
R6 DH10BGFP_pD864_LacZ_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: H3 PGCGROWTHCONDITIONS
synthetic circuit: LACZ PGCGROWTHCONDITIONS
synthetic circuit: Lux PGCGROWTHCONDITIONS
synthetic circuit: M1 PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
treatment: 15 min after induction with rhamnose PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
treatment: 60 min after induction with rhamnose PGCGROWTHCONDITIONS
3C-seq: 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles PGCGROWTHCONDITIONS
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https: PGCGROWTHCONDITIONS
3C-seq of E. coli fis cells in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli fis cells in exponential phase 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli hns cells in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli hns cells in exponential phase 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli hupAB cells in exponential phase 37°C PGCGROWTHCONDITIONS
3C-seq of E. coli hupAB cells in exponential phase 37°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli matP cells in exponential phase 22°C PGCGROWTHCONDITIONS
3C-seq of E. coli matP cells in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli matP cells in exponential phase 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli matPDC20 cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli matPDC20 cells harbouring plasmid pGBM2 in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli matPDC20 cells in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli mukB cells in exponential phase 22°C PGCGROWTHCONDITIONS
3C-seq of E. coli mukB cells in exponential phase 22°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli mukBmatP cells in exponential phase 22°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells harbouring plasmid pGBM2 in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells harbouring plasmid pGBM2 in exponential phase 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 22°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 22°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 30°C -Replicate 2 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 37°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase 37°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase LB 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in exponential phase LB 30°C -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in stationary phase 30°C (30h) PGCGROWTHCONDITIONS
3C-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1 PGCGROWTHCONDITIONS
3C-seq of E. coli zapB cells harbouring plasmid pGBM2-5xmatS in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli zapB cells harbouring plasmid pGBM2 in exponential phase 30°C PGCGROWTHCONDITIONS
3C-seq of E. coli zapB cells in exponential phase 30°C PGCGROWTHCONDITIONS
Assignment to restriction fragment PGCGROWTHCONDITIONS
Binning at 5kb. PGCGROWTHCONDITIONS
E coli cells PGCGROWTHCONDITIONS
E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Filtering, Mapping quality=30, no ambiguous reads PGCGROWTHCONDITIONS
For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U PGCGROWTHCONDITIONS
For RNA-seq: total RNA was extracted using RNeasy Protect Bacteria according to manufacturer instructions (QIAGEN - # 74524) PGCGROWTHCONDITIONS
Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 [delta]fis::frt-kan-frt PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 [delta]hns::frt- kan -frt PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 [delta]matP::frt-cam-frt PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 [delta]mukB::frt- kan PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 [delta]zapB::frt-kan-frt PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 matP[delta]C20::frt-cam-frt PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 phi80+ [delta]hupA::frt- kan -frt [delta]hupB::frt-cam-frt PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1phi80+ [delta]mukB::frt- apra [delta]matP::frt-cam-frt PGCGROWTHCONDITIONS
growth condition: LB at 30°C PGCGROWTHCONDITIONS
growth condition: LB at 37°C PGCGROWTHCONDITIONS
growth condition: MM + 0.12% casaminoacids +0.4% glucose at 22°C PGCGROWTHCONDITIONS
growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive PGCGROWTHCONDITIONS
Library strategy: 3C-seq PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script). PGCGROWTHCONDITIONS
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq of E. coli wt cells in stationary phase 30°C (30h) PGCGROWTHCONDITIONS
RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: rna-seq: genomic position (middle of the 5kb-bin) to each count. 3C seq: contact maps (2D array of 928 5kb-bins x 928 5kb-bins). PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_mRNA_5m_rep1 PGCGROWTHCONDITIONS
emptyvec_mRNA_5m_rep2 PGCGROWTHCONDITIONS
emptyvec_totalRNA_30m_rep1 PGCGROWTHCONDITIONS
emptyvec_totalRNA_30m_rep2 PGCGROWTHCONDITIONS
emptyvec_totalRNA_5m_rep1 PGCGROWTHCONDITIONS
emptyvec_totalRNA_5m_rep2 PGCGROWTHCONDITIONS
ercc spike-in: No PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_mRNA_5m_rep1 PGCGROWTHCONDITIONS
MazF_mRNA_5m_rep2 PGCGROWTHCONDITIONS
MazF_totalRNA_30m_rep1 PGCGROWTHCONDITIONS
MazF_totalRNA_30m_rep2 PGCGROWTHCONDITIONS
MazF_totalRNA_5m_rep1 PGCGROWTHCONDITIONS
MazF_totalRNA_5m_rep2 PGCGROWTHCONDITIONS
MazF_totalRNA_60m_rep1 PGCGROWTHCONDITIONS
MazF_totalRNA_60m_rep2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
ribozero: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 30 minutes PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
time induction: 60 minutes PGCGROWTHCONDITIONS
Bacteria PGCGROWTHCONDITIONS
Culture of bacterial strains (10 mL) were centrifuged 20 min at 10,000 g and bacterial pellets were washed 3 times with 2 mL of phosphate buffered saline (PBS). DNA extraction was performed using the EasyDNA kit (Invitrogen) following the manufacturer instructions slightly modified. Briefly, the bacterial pellet was incubated 5 min in 200 μL of PBS and 1 μL of protéinase K (20 mg PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Fluorescence intensities of oligonucleotide spots were extracted from the scanned images using the Feature Extraction software (V11.0, Agilent Technologies). Then data were processed with dedicated scripts based on C++ and Delphi languages. For each probe, median intensity value of the 3 replicates was conserved and used as the probe signal value. The SNR (Signal-to-Noise Ratio), similar to the detection threshold response (positive hybridization) and corresponding to the probe signal value divided by the local background intensity value, was calculated for each probe. The SNR thresholds were set to 3 for 25-mer probes and 6 for 54-mer probes. Such SNR threshold values ensured a very specific response of the FibroChip, except for genes belonging to very close strains from the same species. Results for 25- and 54-mer probes were treated independently and for each probe type, a gene was considered as detected when 65% of probes were positive. The SNR value of a detected gene was then calculated by the mean of the SNR of all 25- or 54-mer probes targeting this gene, meeting or not the defined SNR threshold. PGCGROWTHCONDITIONS
gDNA_Ecoli_K12 PGCGROWTHCONDITIONS
Genomic DNA was extracted from 4 bacteria strains. Strains Fibrobacter succinogenes S85 (ATCC 19169), Ruminococcus albus 20 (ATCC 27211) and Bacteroides xylanisolvens XB1A (DSM 18836T) were grown 15 h under strictly anaerobic conditions (Hungate, 1950) in a complex medium containing 20% of clarified rumen fluid (Béra-Maillet et al., 2000) and 0.2 g of cellobiose (Sigma-Aldrich) as carbon source, at 39°C for the two first ones and 37°C for the third one. The strain Escherichia coli K12 (ATCC 10798) was cultivated 15 h at 37°C in Luria-Bertani medium under shaking and aerobic conditions. ( PGCGROWTHCONDITIONS
gut origin: Human colon PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
AcrA-Negative, Multidrug Efflux Mutant Strain PGCGROWTHCONDITIONS
AcrB- and EmrAB-Negative, Multidrug Efflux Mutant Strain PGCGROWTHCONDITIONS
AcrB-Negative, Multidrug Efflux Mutant Strain PGCGROWTHCONDITIONS
AG102MB is an isogenic mutant derived from hyper-resistant AG102 (marR1).  It contains a mutation at the acrB locus (marR1, acrB::kan) resulting in a multidrug efflux negative phenotype. PGCGROWTHCONDITIONS
Cultures were grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C. PGCGROWTHCONDITIONS
Cultures were grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C.  Cells were cultured with 25 ug PGCGROWTHCONDITIONS
E. coli AcrA Multidrug Efflux Mutant PGCGROWTHCONDITIONS
E. coli AcrB and EmrAB Multidrug Efflux Double Mutant PGCGROWTHCONDITIONS
E. coli AcrB Multidrug Efflux Mutant PGCGROWTHCONDITIONS
Efflux Mutant Parent Strain PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
HNCE3 is an isogenic mutant derived from hyper-resistant AG102 (marR1).  It contains a nonpolar mutation at the acrA locus which allows read-through for acrB expression and results in a multidrug efflux negative phenotype. PGCGROWTHCONDITIONS
HNCE4 is an isogenic mutant derived from drug sensitive AG102MB (marR1, AcrB::kan). It contains an additional mutation at the emrAB locus (marR1, acrB::kan, emrAB::cat) resulting in a multidrug efflux negative phenotype. PGCGROWTHCONDITIONS
The analyzed data were imported to ArrayTrack (NCTR Center for Toxicoinformatics;http: PGCGROWTHCONDITIONS
The parent strain, AG102, was previously derived from AG100 (K-12).  AG102 is drug hyper-resistant due to a mutation in marR (marR1) which increases expression of MarA, a global regulator, which in turn results in overexpression of the AcrAB-TolC multidrug efflux system. PGCGROWTHCONDITIONS
Total RNA was extracted using Qiagen RNeasy kit. PGCGROWTHCONDITIONS
Alignment: reads were mapped to bespoke reference sequence (DL4201_in_lab_reference_genome (available on series record)) using the default parameters of software Bowtie 2 (Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods, 9, 357-359). PGCGROWTHCONDITIONS
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit. PGCGROWTHCONDITIONS
background strain: BW27784 PGCGROWTHCONDITIONS
Bacterial Cell Lysates PGCGROWTHCONDITIONS
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1 PGCGROWTHCONDITIONS
Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
DL4184 biological repeat 1 RecA ChIP PGCGROWTHCONDITIONS
DL4184 biological repeat 2 RecA ChIP_reanalyzed PGCGROWTHCONDITIONS
DL4201 biological repeat 1 RecA ChIP PGCGROWTHCONDITIONS
DL4201 biological repeat 2 RecA ChIP_reanalyzed PGCGROWTHCONDITIONS
DL5699 biological repeat 1 RecA ChIP PGCGROWTHCONDITIONS
DL5699 biological repeat 2 RecA ChIP PGCGROWTHCONDITIONS
DL6204 biological repeat 1 RecA ChIP PGCGROWTHCONDITIONS
DL6204 biological repeat 2 RecA ChIP PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: DL4201_in_lab_reference_genome (available on series record) PGCGROWTHCONDITIONS
genotype: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX- PGCGROWTHCONDITIONS
genotype: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ:: pal246 cynX::GmR  lacIq  lacZX- PGCGROWTHCONDITIONS
genotype: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX- PGCGROWTHCONDITIONS
genotype: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX- PGCGROWTHCONDITIONS
Normalisation: Counts were normalised by applying a single, sample-specific scaling factor.  To calculate this scaling factor, we implemented the median of ratios normalisation of DESeq software (Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol, 11, R106) using R. PGCGROWTHCONDITIONS
Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M PGCGROWTHCONDITIONS
Raw counts of mapped reads per reference base pair were then calculated using SAMtools software (with parameter –d set to 10^6). PGCGROWTHCONDITIONS
strain: DL4184 PGCGROWTHCONDITIONS
strain: DL4201 PGCGROWTHCONDITIONS
strain: DL5966 PGCGROWTHCONDITIONS
strain: DL6204 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt files of a matrix containing genome position in column 1 and number of depth of mapped reads in column 2. Also, in a CSV file of a matrix containing genome position in column 1 and subsequent coloumns with normalised number of depth of mapped reads (column names have the strain number). CSV file is on the series record. PGCGROWTHCONDITIONS
treatment: induced DNA double strand break PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
AG102 was previously derived from AG100 (K-12). AG102 is drug hyper-resistant due to a mutation in marR (marR1) which increases expression of MarA, a global regulator, which in turn results in overexpression of the AcrAB-TolC multidrug efflux system. PGCGROWTHCONDITIONS
Cholic Acid Treatment PGCGROWTHCONDITIONS
DMSO-Only Treatment PGCGROWTHCONDITIONS
E. coli Cholic Acid Treatment PGCGROWTHCONDITIONS
E. coli Estradiol Treatment PGCGROWTHCONDITIONS
E. coli Hydrocortisone Treatment PGCGROWTHCONDITIONS
E. coli Progesterone Treatment PGCGROWTHCONDITIONS
E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved cholic acid at 1 mM final culture concentration. PGCGROWTHCONDITIONS
E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved estradiol at 1 mM final culture concentration. PGCGROWTHCONDITIONS
E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved hydrocortisone at 1 mM final culture concentration. PGCGROWTHCONDITIONS
E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-dissolved progesterone at 1 mM final culture concentration. PGCGROWTHCONDITIONS
E. coli was grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C in the presence of dimethyl sulfoxide (DMSO)-only steroid carrier. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Estradiol Treatment PGCGROWTHCONDITIONS
Hydrocortisone Treatment PGCGROWTHCONDITIONS
Progesterone Treatment PGCGROWTHCONDITIONS
The analyzed data were imported to ArrayTrack (NCTR Center for Toxicoinformatics.  The raw data were normalized by using median channel (intensity) scaling with no background subtraction. PGCGROWTHCONDITIONS
Total RNA was extracted using Qiagen RNeasy kit. PGCGROWTHCONDITIONS
Bacteria were grown in batch or bioreactor vessels in M9 minimal media supplemented with 0.4% glucose. PGCGROWTHCONDITIONS
DNA extraction: Genomic DNA was isolated and purified according to standard procedures (Ausubel et al. 1994).  Genomic DNA was fragmented by nebulization as described by Girgis et al. PLoS Genetics 3(9): e154 (2007) and purified by phenol PGCGROWTHCONDITIONS
Elements with poor spot morphology or exhibiting uneven hybridization caused by dust particles or scratches, were flagged manually and excluded from further analyses. After local background  subtraction and global normalization relative to the genomic DNA reference, duplicate measurements on the same array were averaged, yielding a single vector for each time-point across a perturbation. The data from all hybridizations were combined into a matrix and scaled relative to each other using quantile-normalization as implemented in the Matlab Bioinformatics  toolbox. Biological duplicates from all experiments were averaged, leading to a single set of time-series data for each perturbation. Seven time-points were assayed for each perturbation, corresponding to 0, 4, 8, 12, 20, 28, and 44 minutes post transition. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
evolved_temperature_Up_0min PGCGROWTHCONDITIONS
evolved_temperature_Up_16min PGCGROWTHCONDITIONS
evolved_temperature_Up_44min PGCGROWTHCONDITIONS
evolved temperature up shift 0min PGCGROWTHCONDITIONS
evolved temperature up shift 16min PGCGROWTHCONDITIONS
evolved temperature up shift 44min PGCGROWTHCONDITIONS
genomic DNA PGCGROWTHCONDITIONS
Genomic DNA served as a universal reference PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
oxygen_down_0min PGCGROWTHCONDITIONS
oxygen_down_12min PGCGROWTHCONDITIONS
oxygen_down_20min PGCGROWTHCONDITIONS
oxygen_down_28min PGCGROWTHCONDITIONS
oxygen_down_44min PGCGROWTHCONDITIONS
oxygen_down_4min PGCGROWTHCONDITIONS
oxygen_down_8min PGCGROWTHCONDITIONS
oxygen down shift, 0min PGCGROWTHCONDITIONS
oxygen down shift, 12min PGCGROWTHCONDITIONS
oxygen down shift, 20min PGCGROWTHCONDITIONS
oxygen down shift, 28min PGCGROWTHCONDITIONS
oxygen down shift, 44min PGCGROWTHCONDITIONS
oxygen down shift, 4min PGCGROWTHCONDITIONS
oxygen down shift, 8min PGCGROWTHCONDITIONS
oxygen_Up_0min PGCGROWTHCONDITIONS
oxygen_Up_12min PGCGROWTHCONDITIONS
oxygen_Up_20min PGCGROWTHCONDITIONS
oxygen_Up_28min PGCGROWTHCONDITIONS
oxygen_Up_44min PGCGROWTHCONDITIONS
oxygen_Up_4min PGCGROWTHCONDITIONS
oxygen_Up_8min PGCGROWTHCONDITIONS
oxygen up shift, 0min PGCGROWTHCONDITIONS
oxygen up shift, 12min PGCGROWTHCONDITIONS
oxygen up shift, 20min PGCGROWTHCONDITIONS
oxygen up shift, 28min PGCGROWTHCONDITIONS
oxygen up shift, 44min PGCGROWTHCONDITIONS
oxygen up shift, 4min PGCGROWTHCONDITIONS
oxygen up shift, 8min PGCGROWTHCONDITIONS
parental_temperature_Up_0min PGCGROWTHCONDITIONS
parental_temperature_Up_16min PGCGROWTHCONDITIONS
parental_temperature_Up_44min PGCGROWTHCONDITIONS
parental temperature up shift 0min PGCGROWTHCONDITIONS
parental temperature up shift 16min PGCGROWTHCONDITIONS
parental temperature up shift 44min PGCGROWTHCONDITIONS
Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 250 C and 370 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition. PGCGROWTHCONDITIONS
RNA extraction: A hot-phenol procedure was used to extract total RNA. Cell pellets were lysed with 500 μl TE (pH8.0), 50 μl 10% SDS and lysozyme (0.5 mg PGCGROWTHCONDITIONS
temperature_down_0min PGCGROWTHCONDITIONS
temperature_down_12min PGCGROWTHCONDITIONS
temperature_down_20min PGCGROWTHCONDITIONS
temperature_down_28min PGCGROWTHCONDITIONS
temperature_down_44min PGCGROWTHCONDITIONS
temperature_down_4min PGCGROWTHCONDITIONS
temperature_down_8min PGCGROWTHCONDITIONS
temperature down shift, 0min PGCGROWTHCONDITIONS
temperature down shift, 12min PGCGROWTHCONDITIONS
temperature down shift, 20min PGCGROWTHCONDITIONS
temperature down shift, 28min PGCGROWTHCONDITIONS
temperature down shift, 44min PGCGROWTHCONDITIONS
temperature down shift, 4min PGCGROWTHCONDITIONS
temperature down shift, 8min PGCGROWTHCONDITIONS
temperature_Up_0min PGCGROWTHCONDITIONS
temperature_Up_12min PGCGROWTHCONDITIONS
temperature_Up_20min PGCGROWTHCONDITIONS
temperature_Up_28min PGCGROWTHCONDITIONS
temperature_Up_44min PGCGROWTHCONDITIONS
temperature_Up_4min PGCGROWTHCONDITIONS
temperature_Up_8min PGCGROWTHCONDITIONS
temperature up shift, 0min PGCGROWTHCONDITIONS
temperature up shift, 12min PGCGROWTHCONDITIONS
temperature up shift, 20min PGCGROWTHCONDITIONS
temperature up shift, 28min PGCGROWTHCONDITIONS
temperature up shift, 44min PGCGROWTHCONDITIONS
temperature up shift, 4min PGCGROWTHCONDITIONS
temperature up shift, 8min PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF104.3.3_u1 PGCGROWTHCONDITIONS
CF104.3.3_u7 PGCGROWTHCONDITIONS
CF104.3.3_y2 PGCGROWTHCONDITIONS
CF104.3.3_y9 PGCGROWTHCONDITIONS
CF108.4B_u1 PGCGROWTHCONDITIONS
CF108.4B_u2 PGCGROWTHCONDITIONS
CF108.4B_y3 PGCGROWTHCONDITIONS
CF108.4B_y8 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http: PGCGROWTHCONDITIONS
CON206.3A_u1 PGCGROWTHCONDITIONS
CON206.3A_u2 PGCGROWTHCONDITIONS
CON206.3A_y1 PGCGROWTHCONDITIONS
CON206.3A_y2 PGCGROWTHCONDITIONS
CON208.3A_u1 PGCGROWTHCONDITIONS
CON208.3A_u8 PGCGROWTHCONDITIONS
CON208.3A_y2 PGCGROWTHCONDITIONS
CON208.3A_y6 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http: PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http: PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Bacterial cells were grown in dYT medium (Miller, JH (1972) Experiments in Molecular Genetics (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY) supplemented with kanamycin (10 mg PGCGROWTHCONDITIONS
E.coli PGCGROWTHCONDITIONS
E. coli B178 groESL(-) expressing human Hsp60 and Hsp10 PGCGROWTHCONDITIONS
E. coli B178 groESL(-) expressing human wt and Val98Ile Hsp60 and Hsp10 PGCGROWTHCONDITIONS
E. coli strain B178 (Georgopoulos et al. (1973) J Mol Biol 76: 45-60) in which the endogenous groES and groEL genes have been deleted and that is maintained alive by the pOFX-tac1-derived plasmid carrying an IPTG-inducible operon with cDNA encoding human Hsp10 and the mature part of human wild type Hsp60 (Hansen et al., 2002). These cells were subsequently transformed by electroporation with a second plasmid, derivative of pBAD PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS5.0 PGCGROWTHCONDITIONS
Total RNA was purified using the RNAeasy kit (Qiagen). PGCGROWTHCONDITIONS
Data were analyzed using custom software based on the R programming environment and BioConductor packages. Each probe was randomly spotted in three to five replicates to control for positional effects on the array. Data from replicate probes were summarized by the median of the log2-transformed intensities. No normalization or background correction was performed. PGCGROWTHCONDITIONS
E.coli CFT073 genomic DNA PGCGROWTHCONDITIONS
E.coli CFT073 genomic DNA hybridization to LLNL virulence mechanism array v2A PGCGROWTHCONDITIONS
E.coli O157:H7 EDL 933 genomic DNA PGCGROWTHCONDITIONS
E.coli O157:H7 EDL 933 genomic DNA hybridization to LLNL virulence mechanism array v2A PGCGROWTHCONDITIONS
Escherichia coli CFT073 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genomic DNA was extracted using the Epicentre DNA extraction kit according to the manufacturer's protocols. PGCGROWTHCONDITIONS
serovar O157:H7 strain EDL933; GenBank accession NC_002655.2 PGCGROWTHCONDITIONS
strain CFT073; GenBank accession AE014075.1 PGCGROWTHCONDITIONS
The bacterial culture pellets were grown according to the instructions from ATCC. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Functional annotation was done using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources 6.7, NIAID, NIH (http: PGCGROWTHCONDITIONS
incubation time: 5 hr PGCGROWTHCONDITIONS
Next, a linear model was built for each comparison using the R LIMMA package and statistics for differential expression analysis were computed. To filter for differential expression, two fold or three-fold change with a FDR ≤0.05 were used as the threshold. PGCGROWTHCONDITIONS
PA20 cultures PGCGROWTHCONDITIONS
PA20 cultures for RNA-seq were grown on T-agar with and without added Sulfamethoxazole-  Trimethoprim at designated levels for the indicated times and temperatures. Working stocks were tested and maintained using LB (Miller formulation) or LB agar. Plasmid pSE380 derivatives were induced by IPTG. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols; rRNAs were removed by Ribozero (gram negative), libraries were prepared using TruSeq protocol. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq data were mapped to the E. coli O157:H7 Sakai genome using the Subjunc aligner program from the Subread package (v1.4.6)   (http: PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
T5_1x_4 PGCGROWTHCONDITIONS
T5_27x_1 PGCGROWTHCONDITIONS
The alignment Bam files were compared against the gene annotation general feature format (GFF) file, and raw counts for each gene were  generated using the featureCounts tool from Subread. The raw counts data of the expressed genes was normalized for RNA composition using the trimmed mean of M values (TMM) method (http: PGCGROWTHCONDITIONS
Total RNA samples were isolated using RNAzol RT (Molecular Research Center) by following manufature's instructions. Contaminating DNA was   removed from RNA samples by DNase I digestion using the TURBO DNA-free kit (Ambion). PGCGROWTHCONDITIONS
15degrees replicate 1 PGCGROWTHCONDITIONS
15degrees replicate 2 PGCGROWTHCONDITIONS
15degrees replicate 3 PGCGROWTHCONDITIONS
46degrees replicate 1 PGCGROWTHCONDITIONS
46degrees replicate 2 PGCGROWTHCONDITIONS
46degrees replicate 3 PGCGROWTHCONDITIONS
BC-7ppm replicate 1 PGCGROWTHCONDITIONS
BC-7ppm replicate 2 PGCGROWTHCONDITIONS
BC-7ppm replicate 3 PGCGROWTHCONDITIONS
BC-9ppm replicate 1 PGCGROWTHCONDITIONS
BC-9ppm replicate 2 PGCGROWTHCONDITIONS
BC-9ppm replicate 3 PGCGROWTHCONDITIONS
CH3COOH (pH 5.9 ± 0.05); HCl (pH 4.75 ± 0.05); NaOH (pH 9.6 ± 0.05); EtOH (5%); NaCl (4.5%); Glycerol (15%); BC (7 and 9 mg PGCGROWTHCONDITIONS
CH3COOH replicate 1 PGCGROWTHCONDITIONS
CH3COOH replicate 2 PGCGROWTHCONDITIONS
CH3COOH replicate 3 PGCGROWTHCONDITIONS
Control replicate 1 PGCGROWTHCONDITIONS
Control replicate 2 PGCGROWTHCONDITIONS
Control replicate 3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
EtBr replicate 1 PGCGROWTHCONDITIONS
EtBr replicate 2 PGCGROWTHCONDITIONS
EtBr replicate 3 PGCGROWTHCONDITIONS
EtOH replicate 1 PGCGROWTHCONDITIONS
EtOH replicate 2 PGCGROWTHCONDITIONS
EtOH replicate 3 PGCGROWTHCONDITIONS
Glycerol replicate 1 PGCGROWTHCONDITIONS
Glycerol replicate 2 PGCGROWTHCONDITIONS
Glycerol replicate 3 PGCGROWTHCONDITIONS
HCl replicate 1 PGCGROWTHCONDITIONS
HCl replicate 3 PGCGROWTHCONDITIONS
NaCl replicate 1 PGCGROWTHCONDITIONS
NaCl replicate 2 PGCGROWTHCONDITIONS
NaCl replicate 3 PGCGROWTHCONDITIONS
NaOH replicate 1 PGCGROWTHCONDITIONS
NaOH replicate 3 PGCGROWTHCONDITIONS
pooled RNA from all conditions including the control, reference PGCGROWTHCONDITIONS
The cultures were prepared by inoculating one colony from tryptone soya agar (TSA) (Oxoid) (overnight growth at 37°C) to 5 ml TSB and incubating overnight at 37°C, with shaking (200 rpm). This culture was initially diluted 1:10 in medium and used to inoculate room-temperature TSB for each of the different stress factors (40 ml total volume) to a final concentration of approx. 1´107 CFU PGCGROWTHCONDITIONS
The fluorescent spot intensities were quantified using ImaGeneÔ 5.6.1 (BioDiscovery Inc.) software. Background subtraction and normalization (LOWESS) was performed in GeneSpringä 7 (Silicon Genetics). (A lowess curve was fit to the log-intensity versus log-ratio plot. 20% of the data was used to calculate the lowess fit at each point. The curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then the value was set to 10). Only data from spots representing E. coli K-12 MG1655 genes were analyzed in our studies. All analyses were based on 3 biological replicates with the exception of the second biological replicate from conditions HCl and NaOH. These two observations were removed due to bad hybridization giving a total of 34 array hybridizations (observations). Genes not present in any of the 34 observations were filtered out, resulting in the analysis of 4279 out of 4289 MG1655 genes on the array. Missing values (data points) were replaced by using the KNNimpute procedure (k=10) on log2 transformed data. PGCGROWTHCONDITIONS
Total RNA was extracted from 1 ml cells using the RNeasy Protect Bacteria Mini Prep kit (Qiagen) as recommended by the manufacturer including the “on-column” DNase treatment. PGCGROWTHCONDITIONS
accession: NC_000913.2+NC_000913.3 PGCGROWTHCONDITIONS
After 0.5 M NaCl treatment for 10 min of the early-exponential phase cells, samples were collected. PGCGROWTHCONDITIONS
After 0.5 M NaCl treatment for 20 min of the early-exponential phase cells, samples were collected. PGCGROWTHCONDITIONS
After 0.5 M NaCl treatment for 45 min of the early-exponential phase cells, samples were collected. PGCGROWTHCONDITIONS
Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction.. PGCGROWTHCONDITIONS
chip antibody: none PGCGROWTHCONDITIONS
chip antibody: RNAP beta subunit antibody PGCGROWTHCONDITIONS
E. coli CC72 was grown in water bath to early-exponential phase (OD600 0.2) at 37°C in LB medium. PGCGROWTHCONDITIONS
E.coli_LB_rep2 PGCGROWTHCONDITIONS
E.coli_LB_rep3 PGCGROWTHCONDITIONS
E.coli_Na10_rep1 PGCGROWTHCONDITIONS
E.coli_Na10_rep2 PGCGROWTHCONDITIONS
E.coli_Na10_rep3 PGCGROWTHCONDITIONS
E.coli_Na20_rep1 PGCGROWTHCONDITIONS
E.coli_Na20_rep2 PGCGROWTHCONDITIONS
E.coli_Na20_rep3 PGCGROWTHCONDITIONS
E.coli_Na45_rep1 PGCGROWTHCONDITIONS
E.coli_Na45_rep2 PGCGROWTHCONDITIONS
E.coli_Na45_rep3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype: Fusion of venus to the 3' end of rpoC in E. coli wild-type MG1655 PGCGROWTHCONDITIONS
RNAP beta subunit ChIP DNA from E. coli CC72 10 min after osmotic stress PGCGROWTHCONDITIONS
RNAP beta subunit ChIP DNA from E. coli CC72 20 min after osmotic stress PGCGROWTHCONDITIONS
RNAP beta subunit ChIP DNA from E. coli CC72 45 min after osmotic stress PGCGROWTHCONDITIONS
RNAP beta subunit ChIP DNA from E. coli CC72 at early-exponential phase PGCGROWTHCONDITIONS
The ChIP experiment was performed essentially as described previously (Herring, Raffaelle et al. 2005). Briefly, the cell cultures were fixed by a 1% formaldehyde and 10 mM sodium phosphate (pH 7.6) solution for 20 min at room temperature. After cell lysis, RNase A treatment and sonication, the chromosome was fragmented to 100-1200 bp. RNAP binding DNA (IP DNA) was immunoprecipitated with RNAP using an antibody against the RNAP β’ subunit and pan mouse magnetic beads. The same sample without the β’ antibody was used as mock immunoprecipitation DNA (mock IP DNA). After washing and de-crosslinking, DNA was purified using the PCR purification kit (Qiagen). PGCGROWTHCONDITIONS
The early-exponential phase cells were collected without NaCl treatment. PGCGROWTHCONDITIONS
A culture volume of 7ml was mixed with the same volume of boiling 2% SDS, 4mM EDTA and heated at 100°C for 3 to 5 minutes then vortexed. At this stage, the extract was either processed further or stored at -20°C. PGCGROWTHCONDITIONS
Affymetrix .CEL files data were normalized with dChip using the array of median brightness (BS). Model method:model-base expression; background substraction: Mismatch Probe (PM PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
exponential phase PGCGROWTHCONDITIONS
JO2057 (WT) PGCGROWTHCONDITIONS
JO2057 (WT), exponential phase, repetition1 PGCGROWTHCONDITIONS
JO2057 (WT), exponential phase, repetition2 PGCGROWTHCONDITIONS
JO2057 WT, LB, exponential phase, repetition1 PGCGROWTHCONDITIONS
JO2057 WT, LB, exponential phase, repetition2 PGCGROWTHCONDITIONS
JO2057 WT, LB, stationary phase, repetition1 PGCGROWTHCONDITIONS
JO2057 WT, LB, stationary phase, repetition2 PGCGROWTHCONDITIONS
JO2057 WT, LB, transition phase PGCGROWTHCONDITIONS
JO2057 (WT), Min Glucose, exponential phase PGCGROWTHCONDITIONS
JO2057 WT, Min Glucose, exponential phase PGCGROWTHCONDITIONS
JO2057 (WT), Min Glucose, stationary phase PGCGROWTHCONDITIONS
JO2057 WT, Min Glucose, stationary phase PGCGROWTHCONDITIONS
JO2057 (WT), Min Glycerol, exponential phase PGCGROWTHCONDITIONS
JO2057 WT, Min Glycerol, exponential phase PGCGROWTHCONDITIONS
JO2057 (WT), Min Glycerol, stationary phase PGCGROWTHCONDITIONS
JO2057 WT, Min Glycerol, stationary phase PGCGROWTHCONDITIONS
JO2057 (WT), stationary phase, repetition1 PGCGROWTHCONDITIONS
JO2057 (WT), stationary phase, repetition2 PGCGROWTHCONDITIONS
JO2057 (WT), transition phase PGCGROWTHCONDITIONS
JO2081 (hupA) PGCGROWTHCONDITIONS
JO2081 (hupA), exponential phase PGCGROWTHCONDITIONS
JO2081 hupA, LB, exponential phase PGCGROWTHCONDITIONS
JO2081 hupA, LB, stationary phase PGCGROWTHCONDITIONS
JO2081 hupA, LB, transition phase PGCGROWTHCONDITIONS
JO2081 (hupA), stationary phase PGCGROWTHCONDITIONS
JO2081 (hupA), transition phase PGCGROWTHCONDITIONS
JO2083 (hupB) PGCGROWTHCONDITIONS
JO2083 (hupB), exponential phase PGCGROWTHCONDITIONS
JO2083 hupB, LB, exponential phase PGCGROWTHCONDITIONS
JO2083 hupB, LB, stationary phase PGCGROWTHCONDITIONS
JO2083 hupB, LB, transition phase PGCGROWTHCONDITIONS
JO2083 (hupB), stationary phase PGCGROWTHCONDITIONS
JO2083 (hupB), transition phase PGCGROWTHCONDITIONS
JO3020 (hupAB) PGCGROWTHCONDITIONS
JO3020 (hupAB), exponential phase, repetition1 PGCGROWTHCONDITIONS
JO3020 (hupAB), exponential phase, repetition2 PGCGROWTHCONDITIONS
JO3020 hupAB, LB, exponential phase, repetition1 PGCGROWTHCONDITIONS
JO3020 hupAB, LB, exponential phase, repetition2 PGCGROWTHCONDITIONS
JO3020 hupAB, LB, stationary phase, repetition1 PGCGROWTHCONDITIONS
JO3020 hupAB, LB, stationary phase, repetition2 PGCGROWTHCONDITIONS
JO3020 hupAB, LB, transition phase PGCGROWTHCONDITIONS
JO3020 (hupAB), Min Glucose, exponential phase PGCGROWTHCONDITIONS
JO3020 hupAB, Min Glucose, exponential phase PGCGROWTHCONDITIONS
JO3020 (hupAB), Min Glucose, stationary phase PGCGROWTHCONDITIONS
JO3020 hupAB, Min Glucose, stationary phase PGCGROWTHCONDITIONS
JO3020 (hupAB), Min Glycerol exponential phase PGCGROWTHCONDITIONS
JO3020 hupAB, Min Glycerol exponential phase PGCGROWTHCONDITIONS
JO3020 (hupAB), Min Glycerol stationary phase PGCGROWTHCONDITIONS
JO3020 hupAB, Min Glycerol stationary phase PGCGROWTHCONDITIONS
JO3020 (hupAB), stationary phase, repetition1 PGCGROWTHCONDITIONS
JO3020 (hupAB), stationary phase, repetition2 PGCGROWTHCONDITIONS
JO3020 (hupAB), transition phase PGCGROWTHCONDITIONS
MW30 (rpoS) PGCGROWTHCONDITIONS
MW30 (rpoS), LB, exponential phase PGCGROWTHCONDITIONS
MW30 rpoS, LB, exponential phase PGCGROWTHCONDITIONS
MW30 (rpoS), LB, stationary phase PGCGROWTHCONDITIONS
MW30 rpoS, LB, stationary phase PGCGROWTHCONDITIONS
Seven mililiter of phenol PGCGROWTHCONDITIONS
stationary phase PGCGROWTHCONDITIONS
The five bacterial strains (JO2057, JO2081, JO2083, JO3020 and MW30) were grown in 100ml LB 0.5% NaCl, M9 minimal glucose or M9 minimal glycerol at 200 rpm in New Brunswick laboratory shaker in 2liter flasks. The typical doubling time, observed in exponential phase in LB, was 40min for JO2057, JO2081, JO2083, MW30 and 75 min for JO3020. After growth curve calibration, the various growth phase sample were collected at the following cell densities: exponential phase: OD600 0.6-0.7; transition: 2.2-2.5 and stationary: 4.6-4.8 (3.0 for hupAB). PGCGROWTHCONDITIONS
transition phase PGCGROWTHCONDITIONS
Anaerobic, minus nitrate, IP PGCGROWTHCONDITIONS
Anaerobic, plus nitrate, IP PGCGROWTHCONDITIONS
Chromatin was extracted and processed according to Oxford Gene Technology protocols (www.ogt.co.uk). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose. PGCGROWTHCONDITIONS
Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose.  PGCGROWTHCONDITIONS
Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose.   PGCGROWTHCONDITIONS
Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose and nitrate.  PGCGROWTHCONDITIONS
Escherichia coli, expressing NsrR with a C-terminal Flag-tag, was grown anaerobically in L broth supplemented with glucose and nitrate.   PGCGROWTHCONDITIONS
NsrR_Flagtag_rep1 PGCGROWTHCONDITIONS
NsrR_Flagtag_rep2 PGCGROWTHCONDITIONS
NsrR_Flagtag_rep3 PGCGROWTHCONDITIONS
The value is the simple linear ratio of the processed Cy3 and Cy5 signals. PGCGROWTHCONDITIONS
The value is the simple linear ratio of the processed Cy5 and Cy3 signals. PGCGROWTHCONDITIONS
bacteria harvested from blood of chickens PGCGROWTHCONDITIONS
condition: in vivo PGCGROWTHCONDITIONS
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US). PGCGROWTHCONDITIONS
E058 in vivo, biological rep1 PGCGROWTHCONDITIONS
E058 in vivo, biological rep2 PGCGROWTHCONDITIONS
E058 in vivo, biological rep3 PGCGROWTHCONDITIONS
E058ΔrstAB in vivo, biological rep1 PGCGROWTHCONDITIONS
E058ΔrstAB in vivo, biological rep2 PGCGROWTHCONDITIONS
E058ΔrstAB in vivo, biological rep3 PGCGROWTHCONDITIONS
Escherichia coli APEC O2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
strain: E058 PGCGROWTHCONDITIONS
The in vivo bacterial samples were harvested with two-step centrifugation. We first centrifuged the collected anticoagulated blood samples at low speed to remove the abundant red and white blood cells and collected the upper serum layer. We then used high-speed centrifugation to precipitate the bacteria from the serum. PGCGROWTHCONDITIONS
To prepare the in vivo samples, the bacteria was harvested from cardiac blood  in 1-day-old chickens at 5 hours post infection. PGCGROWTHCONDITIONS
Total RNA from in vivo samples of APEC E058 and E058ΔrstAB was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
10.FHI9.IND.HUS PGCGROWTHCONDITIONS
11.FHI12.nIND.HUS PGCGROWTHCONDITIONS
12.FHI12.IND.HUS PGCGROWTHCONDITIONS
13.FHI24.nIND.HUS PGCGROWTHCONDITIONS
15.FHI25.nIND.HUS PGCGROWTHCONDITIONS
16.FHI25.IND.HUS PGCGROWTHCONDITIONS
17.FHI27.nIND.HUS PGCGROWTHCONDITIONS
18.FHI27.IND.HUS PGCGROWTHCONDITIONS
19.FHI36.nIND.nHUS PGCGROWTHCONDITIONS
1.FHI4.nIND.HUS PGCGROWTHCONDITIONS
20.FHI36.IND.nHUS PGCGROWTHCONDITIONS
21.FHI43.nIND.nHUS PGCGROWTHCONDITIONS
22.FHI43.IND.nHUS PGCGROWTHCONDITIONS
23.FHI48.nIND.HUS PGCGROWTHCONDITIONS
25.FHI79.nIND.HUS PGCGROWTHCONDITIONS
26.FHI79.IND.HUS PGCGROWTHCONDITIONS
27.FHI95.nIND.nHUS PGCGROWTHCONDITIONS
28.FHI95.IND.nHUS PGCGROWTHCONDITIONS
29.St. Olav40.nIND.nHUS PGCGROWTHCONDITIONS
2.FHI4.IND.HUS PGCGROWTHCONDITIONS
31.St. Olav104.nIND.nHUS PGCGROWTHCONDITIONS
32.St. Olav104.IND.nHUS PGCGROWTHCONDITIONS
33.St. Olav157.nIND.nHUS PGCGROWTHCONDITIONS
34.St. Olav157.IND.nHUS PGCGROWTHCONDITIONS
35.St. Olav172.nIND.nHUS PGCGROWTHCONDITIONS
37.St. Olav174.nIND.nHUS PGCGROWTHCONDITIONS
38.St. Olav174.IND.nHUS PGCGROWTHCONDITIONS
39.St. Olav178.nIND.nHUS PGCGROWTHCONDITIONS
3.FHI6.nIND.HUS PGCGROWTHCONDITIONS
40.St. Olav178.IND.nHUS PGCGROWTHCONDITIONS
41.St. Olav179.nIND.nHUS PGCGROWTHCONDITIONS
42.St. Olav179.IND.nHUS PGCGROWTHCONDITIONS
43.FHI63.nIND.HUS PGCGROWTHCONDITIONS
44.FHI63.IND.HUS PGCGROWTHCONDITIONS
45.FHI66.nIND.nHUS PGCGROWTHCONDITIONS
46.FHI66.IND.nHUS PGCGROWTHCONDITIONS
47.FHI83.nIND.HUS PGCGROWTHCONDITIONS
48.FHI83.IND.HUS PGCGROWTHCONDITIONS
49.St. Olav17.nIND.nHUS PGCGROWTHCONDITIONS
4.FHI6.IND.HUS PGCGROWTHCONDITIONS
50.St. Olav17.IND.nHUS PGCGROWTHCONDITIONS
51.St. Olav39.IND.nHUS PGCGROWTHCONDITIONS
52.St. Olav63.nIND.nHUS PGCGROWTHCONDITIONS
53.St. Olav63.IND.nHUS PGCGROWTHCONDITIONS
54.St. Olav164 .nIND.HUS PGCGROWTHCONDITIONS
55.St. Olav164 .IND.HUS PGCGROWTHCONDITIONS
56.St. Olav176.IND.HUS PGCGROWTHCONDITIONS
57.St. Olav39.nIND.nHUS PGCGROWTHCONDITIONS
59.St. Olav173.IND.nHUS PGCGROWTHCONDITIONS
5.FHI7.nIND.HUS PGCGROWTHCONDITIONS
60.St. Olav176.nIND.HUS PGCGROWTHCONDITIONS
6.FHI7.IND.HUS PGCGROWTHCONDITIONS
7.FHI8.nIND.HUS PGCGROWTHCONDITIONS
8.FHI8.IND.HUS PGCGROWTHCONDITIONS
9.FHI9.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI12 PGCGROWTHCONDITIONS
E. coli strain FHI24 PGCGROWTHCONDITIONS
E. coli strain FHI25 PGCGROWTHCONDITIONS
E. coli strain FHI27 PGCGROWTHCONDITIONS
E. coli strain FHI36 PGCGROWTHCONDITIONS
E. coli strain FHI4 PGCGROWTHCONDITIONS
E. coli strain FHI43 PGCGROWTHCONDITIONS
E. coli strain FHI48 PGCGROWTHCONDITIONS
E. coli strain FHI6 PGCGROWTHCONDITIONS
E. coli strain FHI63 PGCGROWTHCONDITIONS
E. coli strain FHI66 PGCGROWTHCONDITIONS
E. coli strain FHI7 PGCGROWTHCONDITIONS
E. coli strain FHI79 PGCGROWTHCONDITIONS
E. coli strain FHI8 PGCGROWTHCONDITIONS
E. coli strain FHI83 PGCGROWTHCONDITIONS
E. coli strain FHI9 PGCGROWTHCONDITIONS
E. coli strain FHI95 PGCGROWTHCONDITIONS
E. coli strain St. Olav104 PGCGROWTHCONDITIONS
E. coli strain St. Olav157 PGCGROWTHCONDITIONS
E. coli strain St. Olav164  PGCGROWTHCONDITIONS
E. coli strain St. Olav17 PGCGROWTHCONDITIONS
E. coli strain St. Olav172 PGCGROWTHCONDITIONS
E. coli strain St. Olav173 PGCGROWTHCONDITIONS
E. coli strain St. Olav174 PGCGROWTHCONDITIONS
E. coli strain St. Olav176 PGCGROWTHCONDITIONS
E. coli strain St. Olav178 PGCGROWTHCONDITIONS
E. coli strain St. Olav179 PGCGROWTHCONDITIONS
E. coli strain St. Olav39 PGCGROWTHCONDITIONS
E. coli strain St. Olav40 PGCGROWTHCONDITIONS
E. coli strain St. Olav63 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000752975 PGCGROWTHCONDITIONS
genome accession: GCA_000753215 PGCGROWTHCONDITIONS
genome accession: GCA_000753275 PGCGROWTHCONDITIONS
genome accession: GCA_000936225 PGCGROWTHCONDITIONS
genome accession: GCA_000936245 PGCGROWTHCONDITIONS
genome accession: GCA_000936475 PGCGROWTHCONDITIONS
genome accession: GCA_000937275 PGCGROWTHCONDITIONS
genome accession: GCA_000938695 PGCGROWTHCONDITIONS
genome accession: GCA_000938995 PGCGROWTHCONDITIONS
genome accession: GCA_000939195 PGCGROWTHCONDITIONS
genome accession: GCA_000939755 PGCGROWTHCONDITIONS
genome accession: GCA_000939955 PGCGROWTHCONDITIONS
genome accession: GCA_000941395 PGCGROWTHCONDITIONS
genome accession: GCA_000941895 PGCGROWTHCONDITIONS
genome accession: GCA_000946755 PGCGROWTHCONDITIONS
genome accession: GCA_000947315 PGCGROWTHCONDITIONS
genome accession: GCA_000951835 PGCGROWTHCONDITIONS
genome accession: GCA_000951875 PGCGROWTHCONDITIONS
genome accession: GCA_000951915 PGCGROWTHCONDITIONS
genome accession: GCA_000965545 PGCGROWTHCONDITIONS
genome accession: GCA_000965555 PGCGROWTHCONDITIONS
genome accession: GCA_000965575 PGCGROWTHCONDITIONS
genome accession: GCA_000965625 PGCGROWTHCONDITIONS
genome accession: GCA_000965635 PGCGROWTHCONDITIONS
genome accession: GCA_000965655 PGCGROWTHCONDITIONS
genome accession: GCA_000965665 PGCGROWTHCONDITIONS
genome accession: GCA_000965705 PGCGROWTHCONDITIONS
genome accession: GCA_000965715 PGCGROWTHCONDITIONS
genome accession: GCA_000966935 PGCGROWTHCONDITIONS
genome accession: PVRW00000000 PGCGROWTHCONDITIONS
group (hus PGCGROWTHCONDITIONS
induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI12 PGCGROWTHCONDITIONS
strain: FHI24 PGCGROWTHCONDITIONS
strain: FHI25 PGCGROWTHCONDITIONS
strain: FHI27 PGCGROWTHCONDITIONS
strain: FHI36 PGCGROWTHCONDITIONS
strain: FHI4 PGCGROWTHCONDITIONS
strain: FHI43 PGCGROWTHCONDITIONS
strain: FHI48 PGCGROWTHCONDITIONS
strain: FHI6 PGCGROWTHCONDITIONS
strain: FHI63 PGCGROWTHCONDITIONS
strain: FHI66 PGCGROWTHCONDITIONS
strain: FHI7 PGCGROWTHCONDITIONS
strain: FHI79 PGCGROWTHCONDITIONS
strain: FHI8 PGCGROWTHCONDITIONS
strain: FHI83 PGCGROWTHCONDITIONS
strain: FHI9 PGCGROWTHCONDITIONS
strain: FHI95 PGCGROWTHCONDITIONS
strain: St. Olav104 PGCGROWTHCONDITIONS
strain: St. Olav157 PGCGROWTHCONDITIONS
strain: St. Olav164  PGCGROWTHCONDITIONS
strain: St. Olav17 PGCGROWTHCONDITIONS
strain: St. Olav172 PGCGROWTHCONDITIONS
strain: St. Olav173 PGCGROWTHCONDITIONS
strain: St. Olav174 PGCGROWTHCONDITIONS
strain: St. Olav176 PGCGROWTHCONDITIONS
strain: St. Olav178 PGCGROWTHCONDITIONS
strain: St. Olav179 PGCGROWTHCONDITIONS
strain: St. Olav39 PGCGROWTHCONDITIONS
strain: St. Olav40 PGCGROWTHCONDITIONS
strain: St. Olav63 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
Alignment, Quantiatino and Normalization, Differential Expression : We used the SPARTA(version 1) software package for alignment, differential expression analysis, and post-analysis diagnostics. SPARTA is an RNA-Seq package specifically designed for bacterial studies. It uses the Bowtie(version 1.1.1) short read aligner, HTSeq(version 0.6.1) to count gene features, and edgeR for differential expression. PGCGROWTHCONDITIONS
Annotation : The reference genome (Escherichia_coli_cft073.ASM744v1.dna.chromosome.Chromosome.fa) and annotations (Escherichia_coli_cft073.ASM744v1.32.gtf ) were downloaded from EnsemblBacteria PGCGROWTHCONDITIONS
Bacteria PGCGROWTHCONDITIONS
Cells were then lysed with 0.2 µM of lysozyme in TE (10 mM Tris-Cl, 1 mM EDTA, pH 8.0) for 5 min at room temperature, and total RNA was extracted using the RNeasy Mini Kit (Qiagen). DNA contamination was eliminated by treatment with TURBO DNase (Thermo Fisher). Depletion of ribosomal RNA was accomplished with the Ribominus Transcriptome Isolation Kit (Thermo Fisher) followed by ethanol precipitation. PGCGROWTHCONDITIONS
CFT073 +pBAD rep 1 PGCGROWTHCONDITIONS
CFT073 +pBAD rep 2 PGCGROWTHCONDITIONS
CFT073 +pBAD rep 3 PGCGROWTHCONDITIONS
CFT073 +pBAD-tosR rep 1 PGCGROWTHCONDITIONS
CFT073 +pBAD-tosR rep 2 PGCGROWTHCONDITIONS
CFT073 +pBAD-tosR rep 3 PGCGROWTHCONDITIONS
Depletion of ribosomal RNA was accomplished with the Ribominus Transcriptome Isolation Kit (Thermo Fisher) followed by ethanol precipitation. A stranded library was prepared using a ScriptSeq kit (Illumina) using manufacturer’s recommended protocols.  Each sample was tagged with a six nucleotide barcode unique to each sample to allow multiplexing. The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems) following the manufacturer's recommended protocols.  Six samples were sequenced per lane on a 50 cycle single end run on a HiSeq 2500 (Illumina) in high output mode using version 4 reagents. PGCGROWTHCONDITIONS
E. coli CFT073 carrying either pBAD or pBAD-tosR-his6 were cultured overnight in biological triplicates in LB medium containing ampicillin (100 µg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CFT073 E. coli PGCGROWTHCONDITIONS
plasmid: pBAD PGCGROWTHCONDITIONS
plasmid: pBAD-tosR PGCGROWTHCONDITIONS
qC: We checked the quality of the raw reads data for each sample using FastQC (version 0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CFT073 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .xls,  spreadsheet of normalized read counts for each gene for each sample, differential expression data, and annotation PGCGROWTHCONDITIONS
After chilling on ice, each 100-ml culture was mixed with 25 ml ice-cold ethanol PGCGROWTHCONDITIONS
Bacterial cultures PGCGROWTHCONDITIONS
culture temperature: 30 °C for 60 min PGCGROWTHCONDITIONS
culture temperature: 42 °C for 60 min PGCGROWTHCONDITIONS
dnaB-Ts_30°C PGCGROWTHCONDITIONS
dnaB-Ts_42°C PGCGROWTHCONDITIONS
dnaB-Ts ΔahpC_30°C PGCGROWTHCONDITIONS
dnaB-Ts ΔahpC_42°C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
medium: SB broth PGCGROWTHCONDITIONS
Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA was removed from total RNA by using the Ribo-Zero rRNA removal kit. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration , size distribution and quantification of viable sequencing templates via qPCR. PGCGROWTHCONDITIONS
Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K2 BW25113 whole genome using bowtie v0.12.2 PGCGROWTHCONDITIONS
strain: 2429 PGCGROWTHCONDITIONS
strain: 3780 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. PGCGROWTHCONDITIONS
To generate Illumina-compatible sequencing libraries for each sample, molecular indexes were added to each library, allowing samples to be pooled and sequenced on the Illumina HiSeq 2500 with a 1 x 50 bp single-end configuration. More than 250 million reads were generated per sample, and at least 80% bases had quality scores above Q30. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https: PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: 1 MPa for 15 min PGCGROWTHCONDITIONS
stimulus: Control PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg PGCGROWTHCONDITIONS
all cultures were grown in 10 ml LB broth at 37C PGCGROWTHCONDITIONS
bacterial pellet PGCGROWTHCONDITIONS
Control_1 PGCGROWTHCONDITIONS
Control_2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
media: LB broth PGCGROWTHCONDITIONS
NN2_0018_1 PGCGROWTHCONDITIONS
NN2_0018_2 PGCGROWTHCONDITIONS
Omega17_1 PGCGROWTHCONDITIONS
Omega17_2 PGCGROWTHCONDITIONS
Omega76_1 PGCGROWTHCONDITIONS
Omega76_2 PGCGROWTHCONDITIONS
RNA was extracted using Qiagen’s RNeasy minikit Cat#74106 PGCGROWTHCONDITIONS
Samples were background corrected using the normexp() function in the Limma package in R. This was followed by quantile normalization and log2 transformation. PGCGROWTHCONDITIONS
1 ml of overnight culture was prepared for E. coli DY 330 GyrA-SPA or E. coli DY 330 GyrA-SPA MuSGS by seeding 2YT medium supplemented with antibiotics (kanamycin 50 µg PGCGROWTHCONDITIONS
Cfx_IN_10mkM_3 PGCGROWTHCONDITIONS
Cfx_IN_Mu_10mkM_1 PGCGROWTHCONDITIONS
Cfx_IN_Mu_10mkM_2 PGCGROWTHCONDITIONS
Cfx_IP_10mkM_3 PGCGROWTHCONDITIONS
Cfx_IP_Mu_10mkM_1 PGCGROWTHCONDITIONS
Cfx_IP_Mu_10mkM_2 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Ciprofloxacin Rep 1 +A-IP PGCGROWTHCONDITIONS
Ciprofloxacin Rep 1 +A+IP PGCGROWTHCONDITIONS
Ciprofloxacin Rep 2 +A-IP PGCGROWTHCONDITIONS
Ciprofloxacin Rep 2 +A+IP PGCGROWTHCONDITIONS
Ciprofloxacin Rep 3 +A-IP PGCGROWTHCONDITIONS
Ciprofloxacin Rep 3 +A+IP PGCGROWTHCONDITIONS
Cultures (+A and -A) were incubated at 32°C with shaking for additional 15 min, then cells were pelleted by centrifugation at 10°C (4500xg) and resuspended in 10 ml of TES buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl). Washing procedure was repeated twice to remove culture liquid and excess of gyrase poison. PGCGROWTHCONDITIONS
DNA was extracted from resulting supernatant with phenol PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For proteolysis, affinity gel obtained after the last centrifugation step was diluted with TES buffer up to final volume 200 μl, proteinase K (Sigma-Aldrich) was added (0.5 mg PGCGROWTHCONDITIONS
Genome_build: Escherichia coli W3110 MuSGS (on the basis of NC_007779.1). FASTA and GFF are included on series record. PGCGROWTHCONDITIONS
Gyrase Cleavage Sites (GCSs) were called using custom script (GCSs_calling.py, github: https: PGCGROWTHCONDITIONS
Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer). PGCGROWTHCONDITIONS
Microcin B17 Rep 1 +A-IP PGCGROWTHCONDITIONS
Microcin B17 Rep 1 +A+IP PGCGROWTHCONDITIONS
Microcin B17 Rep 2 +A-IP PGCGROWTHCONDITIONS
Microcin B17 Rep 2 +A+IP PGCGROWTHCONDITIONS
Microcin B17 Rep 3 +A-IP PGCGROWTHCONDITIONS
Microcin B17 Rep 3 +A+IP PGCGROWTHCONDITIONS
Microcin_IN_50mkM_3 PGCGROWTHCONDITIONS
Microcin_IN_Mu_10mkM_1 PGCGROWTHCONDITIONS
Microcin_IN_Mu_10mkM_2 PGCGROWTHCONDITIONS
Microcin_IP_50mkM_3 PGCGROWTHCONDITIONS
MIcrocin_IP_Mu_10mkM_1 PGCGROWTHCONDITIONS
Microcin_IP_Mu_10mkM_2 PGCGROWTHCONDITIONS
musgs presence: - PGCGROWTHCONDITIONS
musgs presence: MuSGS PGCGROWTHCONDITIONS
Oxo_IN_120mkM_3 PGCGROWTHCONDITIONS
Oxo_IN_Mu_120mkM_1 PGCGROWTHCONDITIONS
Oxo_IN_Mu_120mkM_2 PGCGROWTHCONDITIONS
Oxo_IP_120mkM_3 PGCGROWTHCONDITIONS
Oxo_IP_Mu_120mkM_1 PGCGROWTHCONDITIONS
Oxo_IP_Mu_120mkM_2 PGCGROWTHCONDITIONS
Oxolinic acid Rep 1 +A-IP PGCGROWTHCONDITIONS
Oxolinic acid Rep 1 +A+IP PGCGROWTHCONDITIONS
Oxolinic acid Rep 2 +A-IP PGCGROWTHCONDITIONS
Oxolinic acid Rep 2 +A+IP PGCGROWTHCONDITIONS
Oxolinic acid Rep 3 +A-IP PGCGROWTHCONDITIONS
Oxolinic acid Rep 3 +A+IP PGCGROWTHCONDITIONS
Raw reads were aligned to the E. coli w3110 MuSGS genome (containing a strong gyrase binding site from bacteriophage Mu) with BWA MEM (default settings) PGCGROWTHCONDITIONS
Resulting SAM files were processed with custom script (SAM_to_coverage_and_N5E_N3E.py, github: https: PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 1 -A-IP PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 1 +A-IP PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 1 +A+IP PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 2 +A-IP PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 2 +A+IP PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 3 +A-IP PGCGROWTHCONDITIONS
Rifampicine Ciprofloxacin Rep 3 +A+IP PGCGROWTHCONDITIONS
RifCfx_IN_Mu_122mkM_10mkM_1 PGCGROWTHCONDITIONS
RifCfx_IN_Mu_122mkM_10mkM_2 PGCGROWTHCONDITIONS
RifCfx_IN_Mu_122mkM_10mkM_3 PGCGROWTHCONDITIONS
RifCfx_IP_Mu_122mkM_10mkM_1 PGCGROWTHCONDITIONS
RifCfx_IP_Mu_122mkM_10mkM_2 PGCGROWTHCONDITIONS
RifCfx_IP_Mu_122mkM_10mkM_3 PGCGROWTHCONDITIONS
Rif_IN_Mu_122mkM_1 PGCGROWTHCONDITIONS
Sequencing libraries were prepared with Accel NGS 1S kit (Swift Bioscience) in accordanse with manufacturer’s protocol. PGCGROWTHCONDITIONS
Starter was cultivated at 32°C with shaking (180 rpm), then was inoculated into 100 ml of 2YT without antibiotics and cultivation was proceeded under the same conditions until culture reaching mid-logphase (OD600=0.6-0.8). PGCGROWTHCONDITIONS
strain: DY330 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tar archives contain the following: PGCGROWTHCONDITIONS
tab-delimited text files with GCSs coordinates, N3E values (\height of the peak\) and GCSs scores (score of the sequence under the GCS obtained after scanning the genome with DNA-gyrase binding motif) PGCGROWTHCONDITIONS
tagged gyrase subunit: GyrA-SPA PGCGROWTHCONDITIONS
text wig files contain coverage depth data PGCGROWTHCONDITIONS
text wig files contain N3E values (number of DNA fragments 3' ends for each position of the genome) PGCGROWTHCONDITIONS
Un_IN_3 PGCGROWTHCONDITIONS
Un_IN_Mu_1 PGCGROWTHCONDITIONS
Un_IN_Mu_2 PGCGROWTHCONDITIONS
Un_IP_3 PGCGROWTHCONDITIONS
Un_IP_Mu_1 PGCGROWTHCONDITIONS
Un_IP_Mu_2 PGCGROWTHCONDITIONS
Untreated Rep 1 -A-IP PGCGROWTHCONDITIONS
Untreated Rep 1 -A+IP PGCGROWTHCONDITIONS
Untreated Rep 2 -A-IP PGCGROWTHCONDITIONS
Untreated Rep 2 -A+IP PGCGROWTHCONDITIONS
Untreated Rep 3 -A-IP PGCGROWTHCONDITIONS
Untreated Rep 3 -A+IP PGCGROWTHCONDITIONS
Washed pellets were resuspended in 1 ml of TESS buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl, 0.02% SDS, 0.2% Tween-20) with addition of proteases inhibitors cocktail (cOmplete ultra EDTA free, Roche) and RNAse A (Thermo Scientific). Resulting suspensions were sonicated with parameters optimized to obtain DNA fragments between 200 and 700 bp (SONOPULS HD 3100). Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer). PGCGROWTHCONDITIONS
When reaching  the optical density indicated (OD600=0.6-0.8) the culture was bisected and DNA gyrase poison (ciprofloxacin, oxolinic acid or microcin B17) was added to the first half (+A samples), while second served as a control (-A samples). PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envz3600 PGCGROWTHCONDITIONS
envz600 PGCGROWTHCONDITIONS
envz900 PGCGROWTHCONDITIONS
envzM1200 PGCGROWTHCONDITIONS
envzM2400 PGCGROWTHCONDITIONS
envzM3600 PGCGROWTHCONDITIONS
envzM600 PGCGROWTHCONDITIONS
envzM900 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1 PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
plasmid: pLCenvZM, pPCB (mutation) PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng PGCGROWTHCONDITIONS
plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
BW25113 sdiA-empty vector 12h biofilm cells at 30oC PGCGROWTHCONDITIONS
BW25113 sdiA-SdiA1E11 12h biofilm cells at 30oC PGCGROWTHCONDITIONS
BW25113 sdiA-WTSdiA 12h biofilm cells at 30oC PGCGROWTHCONDITIONS
Channel 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
mutant SdiA1E11 PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of K-12 sdiA-no SdiA 1 after 12h of growth in LB + 1 mMIPTG and 30 microM Cm with glass wool at 30oC PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of K-12 sdiA-SdiA1E11 after 12h of growth in LB + 1 mMIPTG and 30 microM Cm with glass wool at 30oC PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of K-12 sdiA-WTSdiA after 12h of growth in LB + 1 mMIPTG and 30 microM Cm with glass wool at 30oC PGCGROWTHCONDITIONS
To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia PGCGROWTHCONDITIONS
wild type SdiA PGCGROWTHCONDITIONS
After 50 hours, samples (10 ml) were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.  RNA was quantified using a BioPhotometer (Eppendorf). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3 PGCGROWTHCONDITIONS
Steady-state continuously-cultured control samples in the presence of adequate Zn PGCGROWTHCONDITIONS
Steady-state continuously-cultured experiment samples in the total absence of Zn PGCGROWTHCONDITIONS
Steady-state continuously-cultured experiment samples in total absence of Zn PGCGROWTHCONDITIONS
Steady-state continuously-cultured MG1655 in the presence of adequate Zn PGCGROWTHCONDITIONS
Steady-state continuously-cultured MG1655 in the total absence of Zn PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 1A PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 1B PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 2A PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 2B PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 3A PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli cultured under severe zinc limitation Chemostat 3B PGCGROWTHCONDITIONS
1.Holme T, Arvidson S, Lindholm B, and Pavlu B. 1970. Enzymes: Laboratory-scale production. Process Biochemistry 62-66. PGCGROWTHCONDITIONS
1. Neubauer, A., J. Soini, M. Bollok, M. Zenker, J. Sandqvist, J. Myllyharju, and P. Neubauer. 2007. Fermentation process for tetrameric human collagen prolyl 4-hydroxylase in Escherichia coli: improvement by gene optimisation of the PDI PGCGROWTHCONDITIONS
E.coli W3110, 15 minutes after oxygen downshift, sample S2 PGCGROWTHCONDITIONS
E.coli W3110, 15 minutes before oxygen downshift, sample S1 PGCGROWTHCONDITIONS
E.coli W3110, 45 minutes after oxygen downshift, sample S3 PGCGROWTHCONDITIONS
E.coli W3110, 75 minutes after oxygen downshift, sample S4 PGCGROWTHCONDITIONS
E.coli W3110, fermentation sample taken 15 minutes after oxygen downshift PGCGROWTHCONDITIONS
E.coli W3110, fermentation sample taken 15 minutes before oxygen downshift PGCGROWTHCONDITIONS
E.coli W3110, fermentation sample taken 45 minutes after oxygen downshift PGCGROWTHCONDITIONS
E.coli W3110, fermentation sample taken 75 minutes after oxygen downshift PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GCOS 1.0 PGCGROWTHCONDITIONS
References PGCGROWTHCONDITIONS
References: PGCGROWTHCONDITIONS
Samples for microarray analysis were collected as described earlier [1], (Samples were shortly mixed by vortexing, divided in 0.5 mL aliquots and 1. centrifuged for 3 min at 16,100 ×g and +4 °C. The pellets were resuspended in 250 µL of RNALater (Ambion, USA) and stored at -20 °C until analysis. RNA was extracted using the total RNA kit (A&A Biotechnology, Poland) . PGCGROWTHCONDITIONS
Strain: Escherichia coli W3110 [F– IN(rrnD-rrnE)1] PGCGROWTHCONDITIONS
The cultivations were performed in a Biostat C 15 L bioreactor with the DCU-3 controlling unit and MFCS-win supervisory system (Sartorius) with an initial working volume of 8 L. The mineral salt medium contained per liter: 14.6 g K2HPO4, 3.6 g NaH2PO4 × 2 H2O, 2.0 g Na2SO4, 2.47 g (NH4)2SO4, 0.5 g NH4Cl, 1.0 g (NH4)2-H-citrate, 2 mM MgSO4, 0.1 g thiamine hydrochloride, 0.1 mL antifoam 204 (Sigma) and 2 mL trace element solution (1). The initial glucose concentration was 40 g L-1. The feed solution contained 650 g L-1 glucose. 2 mL L-1 of sterile filtered 1M MgSO4 were added regularly per OD600=10 increase. PGCGROWTHCONDITIONS
Two precultures were performed in LB medium and mineral salt medium with 10 g L 1 of glucose without antifoam agent consecutively at 37 °C at a rotary shaker at 180 rpm. Main cultivations were started as batch cultures at a temperature of 37 °C. The pH was kept at 7.0 by controlled addition of 25% ammonia solution. At the end of the exponential growth phase (cell dry weight about 16 g L-1) the stirrer rate was lowered from 1000 rpm to 500 rpm, to provoke oxygen limitation by decreased oxygen transfer. Constant glucose feed of 100 g L-1 h-1 was started 15 min after the oxygen drop which was enough to ensure glucose excess during the whole cultivation. PGCGROWTHCONDITIONS
Background correction, normalization and calculation of the expression measures were performed using RMA procedure with the WebArray platform (http: PGCGROWTHCONDITIONS
Cell suspension was ammended with 1.25 M sucrose to an osmotic pressure of 2.7 Os kg-1 for 10 minutes. The biomass was centrifuged at 4000 rpm and the pellet treated with RNAProtect (Qiagen) following the manufacturer's protocol. PGCGROWTHCONDITIONS
Cell suspension was ammended with 1.37 M NaCl to obtain an osmotic pressure of 2.7 Os kg-1 for 10 minutes. The biomass was centrifuged at 4000 rpm and the pellet treated with RNAProtect (Qiagen) following the manufacturer's protocol. PGCGROWTHCONDITIONS
E. coli control, biological replicate 1 PGCGROWTHCONDITIONS
E. coli control (biological replicate 2) PGCGROWTHCONDITIONS
E. coli Frag1 (biological replicate 2) PGCGROWTHCONDITIONS
E. coli Frag1 (control sample 1) PGCGROWTHCONDITIONS
E. coli Frag1, hyperosmotic NaCl treatment (biological replicate 1) PGCGROWTHCONDITIONS
E. coli Frag1, NaCl hyperosmotic treatment (biological replicate 2) PGCGROWTHCONDITIONS
E.coli Frag1, sucrose hyperosmotic treatment (biological replicate 1) PGCGROWTHCONDITIONS
E. coli Frag1, sucrose hyperosmotic treatment (biological replicate 2) PGCGROWTHCONDITIONS
E. coli NaCl hyperosmotic treatment (biological replicate 1) PGCGROWTHCONDITIONS
E. coli NaCl hyperosmotic treatment (biological replicate 2) PGCGROWTHCONDITIONS
E. coli, strain Frag1 PGCGROWTHCONDITIONS
E. coli sucrose hyperosmotic treatment (biological replicate 1) PGCGROWTHCONDITIONS
E. coli sucrose hyperosmotic treatment (biological replicate 2) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Grown in Davis's Mineral Salts medium (Gibco BRL Life Technologies Inc.) with 0.1% D-glucose at 25 C (100 r.p.m. shaking) until an OD (550 nm) of 0.6. PGCGROWTHCONDITIONS
No treatment (control sample). PGCGROWTHCONDITIONS
RNA was obtained using the RNAeasy MIDI RNA extraction kit (Qiagen) using lysis buffer containing 0.1% beta-mercaptoethanol. RNA was extracted from lysates and purified according to the manufacturer’s standard protocol and subsequently stored at -80°C. RNA quality was assessed with electrophoresis using a RNA bioanalyser 2100 and Lab RNAChip (Agilent Technologies) before progression to microarray hybridization. PGCGROWTHCONDITIONS
E. coli 15 minute 5 µM cadmium dye swap treatment PGCGROWTHCONDITIONS
E. coli 15 minute 5 µM cadmium treatment PGCGROWTHCONDITIONS
E. coli 15 minute pH only dye swap treatment PGCGROWTHCONDITIONS
E. coli 15 minute pH only treatment PGCGROWTHCONDITIONS
E. coli, 15 minutes, 5 µM cadmium, pH 5 PGCGROWTHCONDITIONS
E. coli, 15 minutes, 5 µM cadmium, pH 7 PGCGROWTHCONDITIONS
E. coli, 15 minutes, no cadmium, pH 5 PGCGROWTHCONDITIONS
E. coli, 15 minutes, no cadmium, pH 7 PGCGROWTHCONDITIONS
E. coli 5 minute 5 µM cadmium dye swap treatment PGCGROWTHCONDITIONS
E. coli 5 minute 5 µM cadmium treatment PGCGROWTHCONDITIONS
E. coli 5 minute pH only dye swap treatment PGCGROWTHCONDITIONS
E. coli 5 minute pH only treatment PGCGROWTHCONDITIONS
E. coli, 5 minutes, 5 µM cadmium, pH 5 PGCGROWTHCONDITIONS
E. coli, 5 minutes, 5 µM cadmium, pH 7 PGCGROWTHCONDITIONS
E. coli, 5 minutes, no cadmium, pH 5 PGCGROWTHCONDITIONS
E. coli, 5 minutes, no cadmium, pH 7 PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7 in the presence of 5.4 µM (1 µg PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7. The cultures were incubated at 25 °C for 15 minutes with manual rotations of the flasks once per minute to resuspend the cells. PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7. The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells. PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose.  The cultures were grown on a rotary shaker (200 rpm) at 37 °C  until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth).  Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes.  The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5 in the presence of 5.4 µM (1 µg PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5 in the presence of 5.4 µM (1 µg PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5. The cultures were incubated at 25 °C for 15 minutes with manual rotations of the flasks once per minute to resuspend the cells. PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5. The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells. PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose.  The cultures were grown on a rotary shaker (200 rpm) at 37 °C  until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth).  Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes.  The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7 in the presence of 5.4 µM (1 µg PGCGROWTHCONDITIONS
E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7 in the presence of 5.4 µM (1 µg PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
MG1655 strain of E. coli K-12 PGCGROWTHCONDITIONS
RNA was extracted and purified using a Masterpure RNA purification kit (Epicentre Technologies). PGCGROWTHCONDITIONS
RNA was extracted and purified using a Masterpure RNA purification kit (Epicentre Technologies).   PGCGROWTHCONDITIONS
Spot intensities and locations were determined using TIGR Spotfinder, Version 3.1.1.  All subsequent analyses were performed using the ma-anova package in the open-source statistical software package, R (www.r-project.org), Version 2.4.1.  The data were normalized using the regional lowess method. PGCGROWTHCONDITIONS
Spot intensities and locations were determined using TIGR Spotfinder, Version 3.1.1. All subsequent analyses were performed using the ma-anova package in the open-source statistical software package, R (www.r-project.org), Version 2.4.1. The data were normalized using the regional lowess method. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 0 hrs using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 1.5 hrs after induction with 0.1 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 1.5 hrs after induction with 0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 1.5 hrs after induction with 1.0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 3.5 hrs after induction with 0.1 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 3.5 hrs after induction with 0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
Cells corresponding to 10 ml culture volume were harvested at 3.5 hrs after induction with 1.0 mM IPTG using centrifugation. The cell pellet was immediately resuspended in RNAlater (Ambion, Austin, TX, USA) and stored at -20°C until further processing. Prior to RNA extraction using MasterPure RNA purification kit (Epicentre, Madison, WI, USA) the pellet was washed in cold phosphate-buffered saline to remove RNAlater. PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after induction with 0.1 mM IPTG PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after induction with 0 mM IPTG PGCGROWTHCONDITIONS
E.coli cells at 1.5 hrs after induction with 1.0 mM IPTG PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of high IPTG (1.0 mM), biological rep2, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of low IPTG (0.1 mM), biological rep2, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after addition of no IPTG (0 mM), biological rep2, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after induction with 0.1 mM IPTG PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after induction with 0 mM IPTG PGCGROWTHCONDITIONS
E.coli cells at 3.5 hrs after induction with 1.0 mM IPTG PGCGROWTHCONDITIONS
E.coli cells at the time of IPTG induction PGCGROWTHCONDITIONS
E.coli cells at the time of IPTG induction (T=0 hrs), biological rep1, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at the time of IPTG induction (T=0 hrs), biological rep1, technical rep2 PGCGROWTHCONDITIONS
E.coli cells at the time of IPTG induction (T=0 hrs), biological rep2, technical rep 1 PGCGROWTHCONDITIONS
E.coli cells at the time of IPTG induction (T=0 hrs), biological rep2, technical rep2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
The probe intensity data  was analyzed using Genetraffic software (Iobion Informatics LLC, La Jolla, CA, USA). The probe intensity data was normalized using GC-RMA algorithm. PGCGROWTHCONDITIONS
Total RNA was extracted using MasterPure RNA purification kits (Epicentre, Madison, WI, USA) according to the manufacturer’s protocol PGCGROWTHCONDITIONS
Acidic Hot Phenol PGCGROWTHCONDITIONS
Cells were grown in M63 glucose (0.2%) minimal media at 37oC at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at an OD600 = 0.3 after being maintained in exponential phase for at least eight generations. PGCGROWTHCONDITIONS
Cells were grown in M63 glucose (0.2%) minimal media at 37oC at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at an OD600 = 1.5. PGCGROWTHCONDITIONS
E. coli K12 grown in M63 glucose (0.2%) minimal media, sampled in exponential phase OD600=0.3 PGCGROWTHCONDITIONS
E. coli K12 grown in M63 glucose (0.2%) minimal media, sampled in stationary phase OD600=1.5 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Exp-rpoS-Rep1 PGCGROWTHCONDITIONS
Exp-rpoS-Rep2 PGCGROWTHCONDITIONS
Exp-rpoS-Rep3 PGCGROWTHCONDITIONS
Exp-WT-Rep1 PGCGROWTHCONDITIONS
Exp-WT-Rep2 PGCGROWTHCONDITIONS
Exp-WT-Rep3 PGCGROWTHCONDITIONS
GCRMA normalized PGCGROWTHCONDITIONS
MG1655 rpoS mutants PGCGROWTHCONDITIONS
MG1655 wild type PGCGROWTHCONDITIONS
Stat-rpoS-Rep1 PGCGROWTHCONDITIONS
Stat-rpoS-Rep2 PGCGROWTHCONDITIONS
Stat-rpoS-Rep3 PGCGROWTHCONDITIONS
Stat-WT-Rep1 PGCGROWTHCONDITIONS
Stat-WT-Rep2 PGCGROWTHCONDITIONS
Stat-WT-Rep3 PGCGROWTHCONDITIONS
Ambion RiboPure RNA Isolation PGCGROWTHCONDITIONS
Ambion RiboPure RNA Isolation  PGCGROWTHCONDITIONS
Data has not been processed other than those protocols within GCOSv1.4 PGCGROWTHCONDITIONS
E. coli 8624 PGCGROWTHCONDITIONS
E. coli 8624 qseF deletion mutant PGCGROWTHCONDITIONS
E. coli 8624 WT PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli 8624 grown in DMEM PGCGROWTHCONDITIONS
Escherichia coli 8624 qseF deletion mutant PGCGROWTHCONDITIONS
Escherichia coli 8624 qseF deletion mutant grown in DMEM media PGCGROWTHCONDITIONS
strain: Escherichia coli 8624 PGCGROWTHCONDITIONS
Aerobic E. coli exposed to CO-RMs for 15 minutes PGCGROWTHCONDITIONS
Aerobic E. coli not exposed to CO-RMs for 15 minutes (control cells) PGCGROWTHCONDITIONS
Aerobic MG1655 exposed to CO-RMs for 15 minutes PGCGROWTHCONDITIONS
Aerobic MG1655 not exposed to CO-RMs for 15 minutes (control cells) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 1a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 1b PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 2a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 2b PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 3a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 3b PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 4a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to aerobically growing cells- Sample 4b PGCGROWTHCONDITIONS
Samples (30 ml) were harvested directly into cold phenol ethanol (187 µl phenol, 3.56 ml ethanol) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by suppliers. RNA was quantified using a BioPhotometer (Eppendorf). PGCGROWTHCONDITIONS
Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3 PGCGROWTHCONDITIONS
Anaerobic E. coli exposed to CO-RMs for 15 minutes PGCGROWTHCONDITIONS
Anaerobic E. coli not exposed to CO-RMs for 15 minutes (control cells) PGCGROWTHCONDITIONS
Anaerobic E. coli were exposed to CO-RMs for 15 minutes PGCGROWTHCONDITIONS
Anaerobic MG1655 exposed to CO-RMs for 15 minutes PGCGROWTHCONDITIONS
Anaerobic MG1655 not exposed to CO-RMs for 15 minutes (control cells) PGCGROWTHCONDITIONS
Anaerobic MG1655 were exposed to CO-RMs for 15 minutes PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 1a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 1b PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 2a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 2b PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 3a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 3b PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 4a PGCGROWTHCONDITIONS
Escherichia coli after addition of CO-RMs to anaerobically growing cells- Sample 4b PGCGROWTHCONDITIONS
Samples (30 ml) were harvested directly into cold phenol ethanol (187 µl phenol, 3.56 ml ethanol) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by suppliers. RNA was quantified using a BioPhotometer (Eppendorf). PGCGROWTHCONDITIONS
Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3 PGCGROWTHCONDITIONS
Bexp_Bstat_dyeswap1 PGCGROWTHCONDITIONS
Bexp_Bstat_dyeswap2 PGCGROWTHCONDITIONS
Bexp_Bstat_rep1 PGCGROWTHCONDITIONS
Bexp_Bstat_rep2 PGCGROWTHCONDITIONS
Bexp_Kexp_dyeswap1 PGCGROWTHCONDITIONS
Bexp_Kexp_dyeswap2 PGCGROWTHCONDITIONS
Bexp_Kexp_rep1 PGCGROWTHCONDITIONS
Bexp_Kexp_rep2 PGCGROWTHCONDITIONS
Bexp_Kstat_dyeswap1 PGCGROWTHCONDITIONS
Bexp_Kstat_dyeswap2 PGCGROWTHCONDITIONS
Bexp_Kstat_rep1 PGCGROWTHCONDITIONS
Bexp_Kstat_rep2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Following background subtraction, spot signal intensities were calculated as percentages of total signal intensities of Cy-3 or Cy-5 signals on each microarray, as a means of normalization. Spots with low intensities were excluded. PGCGROWTHCONDITIONS
MG1655, exponential phase, LB PGCGROWTHCONDITIONS
MG1655, stationary phase, LB PGCGROWTHCONDITIONS
REL606, exponential phase, LB PGCGROWTHCONDITIONS
REL606, stationary phase, LB PGCGROWTHCONDITIONS
Total RNA was isolated from cells grown in LB medium using the Qiagen RNeasy column. PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_arcA_1%_isobutanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli ko-arcA grown in MOPS PGCGROWTHCONDITIONS
Ecoli ko-arcA grown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_fur_1%_isobutanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli ko-fur grown in MOPS PGCGROWTHCONDITIONS
Ecoli ko-fur grown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli ko-furgrown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_ihfA_1%_isobutanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli ko-ihfA grown in MOPS PGCGROWTHCONDITIONS
Ecoli ko-ihfA grown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_phoB_1%_isobutanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli ko-phoB grown in MOPS PGCGROWTHCONDITIONS
Ecoli ko-phoB grown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli_ko_ubiE_1%_isobutanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_ubiE_1%_isobutanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_ko_ubiE_1%_isobutanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_ko_ubiE_1%_isobutanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli ko-ubiE grown in MOPS PGCGROWTHCONDITIONS
Ecoli ko-ubiE grown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_butanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample5_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_1%_isobutanol_Sample5_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_3%_ethanol_Sample4_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_calibration_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_calibration_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_wildtype_calibration_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_wildtype_calibration_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli wildtype grown in MOPS PGCGROWTHCONDITIONS
Ecoli wildtype grown in MOPS, 10 minutes after 1% butanol treatment PGCGROWTHCONDITIONS
Ecoli wildtype grown in MOPS, 10 minutes after 1% isobutanol treatment PGCGROWTHCONDITIONS
Ecoli wildtype grown in MOPS, 10 minutes after 3% ethanol treatment PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Qiagen RNeasy Midikit PGCGROWTHCONDITIONS
Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files.  The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu PGCGROWTHCONDITIONS
RNA from 1% isobutanol treated sample and untreated sample were mixed after RNA purification PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Strain:BW25113 PGCGROWTHCONDITIONS
Strain: BW25113 PGCGROWTHCONDITIONS
Treated with 1% vol PGCGROWTHCONDITIONS
Treated with 3% vol PGCGROWTHCONDITIONS
BW25113, H2O2 PGCGROWTHCONDITIONS
BW25113, water (negative control) PGCGROWTHCONDITIONS
BW25113 ychH, H2O2 PGCGROWTHCONDITIONS
BW25113 ychH, water (negative control) PGCGROWTHCONDITIONS
BW25113 ygiW, H2O2 PGCGROWTHCONDITIONS
BW25113 ygiW, water (negative control) PGCGROWTHCONDITIONS
Channel 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
RNA extracted from cells of BW25113 at OD 1.0 after contacting for 10 min with 2 mM H2O2 in LB at 37oC. PGCGROWTHCONDITIONS
RNA extracted from cells of BW25113 at OD 1.0 after contacting for 10 min with water (negative control) in LB at 37oC. PGCGROWTHCONDITIONS
RNA extracted from cells of BW25113 ychH at OD 1.0 after contacting for 10 min with 2 mM H2O2 in LB at 37oC. PGCGROWTHCONDITIONS
RNA extracted from cells of BW25113 ychH at OD 1.0 after contacting for 10 min with water (negative control) in LB at 37oC. PGCGROWTHCONDITIONS
RNA extracted from cells of BW25113 ygiW at OD 1.0 after contacting for 10 min with 2 mM H2O2 in LB at 37oC. PGCGROWTHCONDITIONS
RNA extracted from cells of BW25113 ygiW at OD 1.0 after contacting for 10 min with water (negative control) in LB at 37oC. PGCGROWTHCONDITIONS
RNA extracted from cells of TG1 PGCGROWTHCONDITIONS
To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown with vigorous shaking at 37 °C to mid-log (light scattering at 600 nm equivalent to 0.4 OD). Sodium phosphate (1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA control PGCGROWTHCONDITIONS
Genomic DNA control from E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
Genomic DNA control from E. coli K-12 MG1655 cells treated with 100ug PGCGROWTHCONDITIONS
Genomic DNA control from E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
Genomic DNA control from E. coli K-12 MG1655 HA3::nusG cells PGCGROWTHCONDITIONS
Monoclonal antibody for HA (12CA5) PGCGROWTHCONDITIONS
Monoclonal antibody for NusA (1NA1) PGCGROWTHCONDITIONS
Monoclonal antibody for RNA polymerase Beta' subunit (NT73) PGCGROWTHCONDITIONS
Monoclonal antibody for Sigma70 (2G10) PGCGROWTHCONDITIONS
NusA ChIP-chip in E. coli K-12 MG1655 cells (Dataset 56226) PGCGROWTHCONDITIONS
NusA ChIP-chip in E. coli K-12 MG1655 cells (Dataset 61392) PGCGROWTHCONDITIONS
NusA ChIP-chip in E. coli K-12 MG1655 cells (Dataset 64131) PGCGROWTHCONDITIONS
NusA ChIP in E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
NusG ChIP-chip in E. coli K-12 MG1655 cells (Dataset 70568) PGCGROWTHCONDITIONS
NusG ChIP-chip in E. coli K-12 MG1655 HA3::nusG cells (Dataset 62261) PGCGROWTHCONDITIONS
NusG ChIP-chip in E. coli K-12 MG1655 HA3::nusG cells (Dataset 62263) PGCGROWTHCONDITIONS
NusG ChIP in E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
NusG ChIP in E. coli K-12 MG1655 HA3::nusG cells PGCGROWTHCONDITIONS
Polyclonal antibody for NusG (raised for this study) PGCGROWTHCONDITIONS
Polyclonal antibody for Rho (gift from Jeff Roberts) PGCGROWTHCONDITIONS
Rho ChIP-chip in E. coli K-12 MG1655 cells (Dataset 3421602) PGCGROWTHCONDITIONS
Rho ChIP-chip in E. coli K-12 MG1655 cells (Dataset 70261) PGCGROWTHCONDITIONS
Rho ChIP in E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells (Dataset 100040) PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells (Dataset 56706) PGCGROWTHCONDITIONS
RNA polymerase (Beta’) ChIP-chip in E. coli K-12 MG1655 cells (Dataset 62215) PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 100ug PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
RNA polymerase (Beta’) ChIP in E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells treated with 100ug PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
Sigma70 ChIP-chip in E. coli K-12 MG1655 cells (Dataset 56859) PGCGROWTHCONDITIONS
Sigma70 ChIP-chip in E. coli K-12 MG1655 cells (Dataset 62214) PGCGROWTHCONDITIONS
Sigma70 ChIP-chip in E. coli K-12 MG1655 cells (Dataset 64194) PGCGROWTHCONDITIONS
Sigma70 ChIP-chip in E. coli K-12 MG1655 cells treated with 100ug PGCGROWTHCONDITIONS
Sigma70 ChIP in E. coli K-12 MG1655 cells PGCGROWTHCONDITIONS
Sigma70 ChIP in E. coli K-12 MG1655 cells treated with 100ug PGCGROWTHCONDITIONS
Strain MG1655 or isogenic strain MG1655 HA3::nusG cells were grown in MOPS minimal medium supplemented with 0.2% glucose (www.genome.wisc.edu PGCGROWTHCONDITIONS
VALUE=log2(Cy3_signal PGCGROWTHCONDITIONS
VALUE=log2(Cy5_signal PGCGROWTHCONDITIONS
E.coli_15min_AE_1 PGCGROWTHCONDITIONS
E.coli_15min_AE_2 PGCGROWTHCONDITIONS
E.coli_15min_aerobic PGCGROWTHCONDITIONS
E.coli_15min_ANA_1 PGCGROWTHCONDITIONS
E. coli_15min_ANA_2 PGCGROWTHCONDITIONS
E. coli_15min_anaerobic PGCGROWTHCONDITIONS
E.coli_15min_anaerobic PGCGROWTHCONDITIONS
E.coli_15min_CORM-2 treated_aerobic PGCGROWTHCONDITIONS
E.coli_15min_CORM-2 treated_anaerobic PGCGROWTHCONDITIONS
E.coli_15min_CORM_AE_1 PGCGROWTHCONDITIONS
E.coli_15min_CORM_AE_2 PGCGROWTHCONDITIONS
E.coli_15min_CORM_ANA_1 PGCGROWTHCONDITIONS
E.coli_15min_CORM_ANA_2 PGCGROWTHCONDITIONS
Escherichia coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Scanned arrays were analyzed with Affymetrix GCOS 1.4 software to obtain Detection calls and Expression values based on MAS 5.0 algorithms. All arrays were scaled to a target value of 500. PGCGROWTHCONDITIONS
The hot-phenol method was used to extract total RNA from two independent cultures of cells grown aerobically PGCGROWTHCONDITIONS
The hot-phenol method was used to extract total RNA from two independent cultures of cells grown aerobically and treated with 250 μM CORM-2 during 15 min. PGCGROWTHCONDITIONS
The hot-phenol method was used to extract total RNA from two independent cultures of cells grown anaerobically PGCGROWTHCONDITIONS
The hot-phenol method was used to extract total RNA from two independent cultures of cells grown anaerobically and treated with 250 μM CORM-2 during 15 min. PGCGROWTHCONDITIONS
Acid adaptation was done in DMEM at pH 5.0 at room temperature, followed by acid-stress at pH 3.0 for 30 minutes PGCGROWTHCONDITIONS
Acid shocking was done in DMEM at pH 3.0 at room temperature for 30 minutes PGCGROWTHCONDITIONS
Acid shocking was done in DMEM at pH 3.0 (unbuffered) at room temperature for 15 minutes PGCGROWTHCONDITIONS
Bacteria were grown in LB broth overnight and subcultured in DMEM PGCGROWTHCONDITIONS
Bacteria were grown in LB broth overnight and subcultured in DMEM prior to acid stress PGCGROWTHCONDITIONS
Control treatment. Bacteria were grown in DMEM pH 7.4 (unstressed) PGCGROWTHCONDITIONS
Cy3 labeled EHEC grown in DMEM pH 7.4 PGCGROWTHCONDITIONS
Cy3 labeled EHEC grown in DMEM pH 7.4, 15 minutes PGCGROWTHCONDITIONS
Cy5 labeled EHEC acid-adapted in DMEM pH 5, followed by 30 minutes pH 3 PGCGROWTHCONDITIONS
Cy5 labeled EHEC acid-stressed in DMEM pH 3, 15 minutes PGCGROWTHCONDITIONS
Cy5 labeled EHEC acid-stressed in DMEM pH 3, 30minutes PGCGROWTHCONDITIONS
EHEC strain 86-24 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) PGCGROWTHCONDITIONS
Signal intensities were averaged among the technical replicates.  Two types of data analysis were performed: to indentify density-dependent changes in gene expression, single averaged normalized signal intensities for each treatment point were compared to the average of corresponding unstressed control signal intensities.  Genes which showed a relative signal log2ratio (SLR) value above 1.0 or below -1.0 were selected for further analysis.  PGCGROWTHCONDITIONS
Signal intensities were averaged among the technical replicates. Two types of data analysis were performed: to indentify density-dependent changes in gene expression, single averaged normalized signal intensities for each treatment point were compared to the average of corresponding unstressed control signal intensities. Genes which showed a relative signal log2ratio (SLR) value above 1.0 or below -1.0 were selected for further analysis.  PGCGROWTHCONDITIONS
Treatment 1: UA30 (EHEC 86-24 exposed to pH 3 for 30 min) PGCGROWTHCONDITIONS
Treatment 2: AA30 (EHEC 86-24 pH 5.0, followed by 30 min pH 3.0) PGCGROWTHCONDITIONS
Treatment 3: UA15 (EHEC 86-24 exposed to pH 3 for 15 min) PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
BW25113 mqsR mutant at OD600=0.5 LB 37C suspension cell PGCGROWTHCONDITIONS
BW25113 wt at OD600=0.5 LB 37C suspension cell PGCGROWTHCONDITIONS
Chipchip BW25113 PGCGROWTHCONDITIONS
E. coli K-12 BW25113 PGCGROWTHCONDITIONS
E. coli K-12 BW25113 mqsR mutant at OD600=0.5 LB 37C suspension cell PGCGROWTHCONDITIONS
E. coli K-12 BW25113 wt at OD600=0.5 LB 37C suspension cell PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
His-tagged DNA extracted from biofilm cells of E. coli K-12 wild type BW25113 PGCGROWTHCONDITIONS
His-tagged DNA extracted from planktonic cells of E. coli K-12 wild type BW25113 PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
RNA extracted from suspension cells of E. coli K-12 BW25113 PGCGROWTHCONDITIONS
RNA extracted from suspension cells of E. coli K-12 BW25113 mqsR deleted mutant after OD600=0.5 of growth in LB at 37oC PGCGROWTHCONDITIONS
RNA extracted from suspension cells of E. coli K-12 BW25113 wild type after OD600=0.5 of growth in LB at 37oC PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 24 h at 37oC with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0oC. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0oC. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.5 at 37oC under 2 mM IPTG with shaking (250 rpm), the planktonic cells were quickly removed and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.5 at 37oC with shaking (250 rpm), the planktonic cells were quickly removed and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.8 at 37oC with shaking (250 rpm), adding 0.5% L-arabinose and incubated for 24 h PGCGROWTHCONDITIONS
10,000U Pencillin G in media PGCGROWTHCONDITIONS
72hr colony growth equiv. to wildtype colony size PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. W3110 PGCGROWTHCONDITIONS
L-form, brain heart infusion agar+Sucrose+MgSO4+Pen G, rep 1 PGCGROWTHCONDITIONS
L-form, brain heart infusion agar+Sucrose+MgSO4+Pen G, rep 2 PGCGROWTHCONDITIONS
L-form, brain heart infusion agar+Sucrose+MgSO4+Pen G, rep 3 PGCGROWTHCONDITIONS
L-form colony morphology PGCGROWTHCONDITIONS
MasterPure RNA purification Kit PGCGROWTHCONDITIONS
overnight colony growth PGCGROWTHCONDITIONS
strain: L-form PGCGROWTHCONDITIONS
strain: wildtype PGCGROWTHCONDITIONS
The data were analyzed with GCOS 1.4 software.  All probe sets scaling was performed with a target signal value of 500.  No normalization was performed. PGCGROWTHCONDITIONS
wildtype, brain heart infusion agar, rep 1 PGCGROWTHCONDITIONS
wildtype, brain heart infusion agar, rep 2 PGCGROWTHCONDITIONS
wildtype, brain heart infusion agar, rep 3 PGCGROWTHCONDITIONS
wildtype, brain heart infusion agar +Sucrose+MgSO4, rep 1 PGCGROWTHCONDITIONS
wildtype, brain heart infusion agar +Sucrose+MgSO4, rep 2 PGCGROWTHCONDITIONS
wildtype, brain heart infusion agar +Sucrose+MgSO4, rep 3 PGCGROWTHCONDITIONS
wildtype colony morphology PGCGROWTHCONDITIONS
Ambion RiboPure RNA Isolation PGCGROWTHCONDITIONS
Data included in file has not been processed other than those protocols within GCOSv1.4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli 8624 PGCGROWTHCONDITIONS
Escherichia coli 8624 grown in DMEM with AI3 PGCGROWTHCONDITIONS
Escherichia coli 8624 grown in DMEM with Epinephrine PGCGROWTHCONDITIONS
Escherichia coli 8624 grown in LB PGCGROWTHCONDITIONS
Escherichia coli 8624 in LB PGCGROWTHCONDITIONS
Escherichia coli 8624 kdpE deletion mutant PGCGROWTHCONDITIONS
Escherichia coli 8624 kdpE deletion mutant grown in DMEM PGCGROWTHCONDITIONS
Escherichia coli 8624 qseB deletion mutant PGCGROWTHCONDITIONS
Escherichia coli 8624 qseB deletion mutant grown in DMEM PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC deletion mutant grown in DMEM PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC deletion mutant grown in DMEM with AI3 PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC deletion mutant grown in DMEM with Epinephrine PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC mutant grown in  LB PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC mutant in DMEM PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC mutant in DMEM with AI3 PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC mutant in DMEM with epinephrine PGCGROWTHCONDITIONS
Escherichia coli 8624 qseC mutant in LB PGCGROWTHCONDITIONS
grown to OD600=1.0 in DMEM PGCGROWTHCONDITIONS
grown to OD600=1.0 in DMEM with 50 uM epinephrine PGCGROWTHCONDITIONS
grown to OD600=1.0 in DMEM with AI3 PGCGROWTHCONDITIONS
grown to OD600=1.0 in DMEM with AI3 signaling molecule PGCGROWTHCONDITIONS
grown to OD600=1.0 in DMEM with Epinephrine PGCGROWTHCONDITIONS
grown to OD600=1.0 in LB PGCGROWTHCONDITIONS
strain: Escherichia coli 8624 PGCGROWTHCONDITIONS
strain: Escherichia coli strain 8624 PGCGROWTHCONDITIONS
strain: Escherichia coli strain 8624 kdpE mutant PGCGROWTHCONDITIONS
strain: Escherichia coli strain 8624 qseB mutant PGCGROWTHCONDITIONS
strain: Escherichia coli strain 8624 qseC PGCGROWTHCONDITIONS
strain: Escherichia coli strain 8624 qseC mutant PGCGROWTHCONDITIONS
E. coli strain B-a PGCGROWTHCONDITIONS
E. coli strain B-b PGCGROWTHCONDITIONS
E. coli strain B DNA PGCGROWTHCONDITIONS
E. coli strain K12-a PGCGROWTHCONDITIONS
E. coli strain K12-b PGCGROWTHCONDITIONS
E. coli strain K12-c PGCGROWTHCONDITIONS
E. coli strain K12-d PGCGROWTHCONDITIONS
E. coli strain K12 DNA PGCGROWTHCONDITIONS
Escherichia coli B PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genomic bacterial DNA was extracted following the protocol described in Maniatis Sambrook (Sambrook et al., 1989). DNA was sonicated in a Bioruptor (Diagenode, Liege, Belgium) to obtain fragments of approximately 500 bp. PGCGROWTHCONDITIONS
Signals of each slide were smoothed using the NMPP program (Wang et al., 2006). Normalisation per chip to 50th percentile and further analyses were performed in GeneSpring GX v7.3.1 (Agilent Technologies, Basel, Switzerland). PGCGROWTHCONDITIONS
strain: B PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Adenosine addition PGCGROWTHCONDITIONS
Alanine addition PGCGROWTHCONDITIONS
Amino acid or nucleotide added to final concentration of 1 mM not exceeding 1 PGCGROWTHCONDITIONS
Arginine addition PGCGROWTHCONDITIONS
Aspartate addition PGCGROWTHCONDITIONS
Cysteine addition PGCGROWTHCONDITIONS
Cytidine addition PGCGROWTHCONDITIONS
E. coli cells 0 min before perturbation PGCGROWTHCONDITIONS
E. coli cells 10 min after specific perturbation PGCGROWTHCONDITIONS
E. coli cells grown to mid-exponential phase after 6-8 generations after stationary phase in M9 minimal medium + 0.4 % glucose. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Glutamate addition PGCGROWTHCONDITIONS
Glutamine addition PGCGROWTHCONDITIONS
Glycine addition PGCGROWTHCONDITIONS
Guanosine addition PGCGROWTHCONDITIONS
Histidine addition PGCGROWTHCONDITIONS
Images were quantified using GenePix Pro software PGCGROWTHCONDITIONS
Isoleucine addition PGCGROWTHCONDITIONS
Lysine addition PGCGROWTHCONDITIONS
Median of intensity data was extracted, LOESS normalized and an ANOVA model was fit using the MAANOVA package in R. The Log (Cy5 PGCGROWTHCONDITIONS
Methionine addition PGCGROWTHCONDITIONS
Phenylalanine addition PGCGROWTHCONDITIONS
Proline addition PGCGROWTHCONDITIONS
Serine addition PGCGROWTHCONDITIONS
stress: Adenosine addition PGCGROWTHCONDITIONS
stress: Alanine addition PGCGROWTHCONDITIONS
stress: Arginine addition PGCGROWTHCONDITIONS
stress: Aspartate addition PGCGROWTHCONDITIONS
stress: control (before perturbation) PGCGROWTHCONDITIONS
stress: Cysteine addition PGCGROWTHCONDITIONS
stress: Cytidine addition PGCGROWTHCONDITIONS
stress: Glutamate addition PGCGROWTHCONDITIONS
stress: Glutamine addition PGCGROWTHCONDITIONS
stress: Glycine addition PGCGROWTHCONDITIONS
stress: Guanosine addition PGCGROWTHCONDITIONS
stress: Histidine addition PGCGROWTHCONDITIONS
stress: Isoleucine addition PGCGROWTHCONDITIONS
stress: Lysine addition PGCGROWTHCONDITIONS
stress: Methionine addition PGCGROWTHCONDITIONS
stress: Phenylalanine addition PGCGROWTHCONDITIONS
stress: Proline addition PGCGROWTHCONDITIONS
stress: Serine addition PGCGROWTHCONDITIONS
stress: Threonine addition PGCGROWTHCONDITIONS
stress: Thymidine addition PGCGROWTHCONDITIONS
stress: Tryptophan addition PGCGROWTHCONDITIONS
stress: Uridine addition PGCGROWTHCONDITIONS
stress: Valine addition PGCGROWTHCONDITIONS
Threonine addition PGCGROWTHCONDITIONS
Thymidine addition PGCGROWTHCONDITIONS
Total RNA extracted using Qiagen RNEASY kit according to directions PGCGROWTHCONDITIONS
Tryptophan addition PGCGROWTHCONDITIONS
Uridine addition PGCGROWTHCONDITIONS
Valine addition PGCGROWTHCONDITIONS
antibody: IgG PGCGROWTHCONDITIONS
antibody: RNAP beta subunit (NT63) PGCGROWTHCONDITIONS
Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug PGCGROWTHCONDITIONS
condition: heat-shocked condition without rifampicin treatment PGCGROWTHCONDITIONS
condition: mid-exponential condition without rifampicin treatment PGCGROWTHCONDITIONS
condition: mid-exponential condition with rifampicin treatment PGCGROWTHCONDITIONS
condition: nitrogen-limiting condition without rifampicin treatment PGCGROWTHCONDITIONS
condition: stationary condition without rifampicin treatment PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by normal mouse IgG (Upstate) for the control (mock-IP). PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by NT63 mouse antibody. PGCGROWTHCONDITIONS
E.coli_heat_dynamic_1 PGCGROWTHCONDITIONS
E.coli_heat_dynamic_2 PGCGROWTHCONDITIONS
E.coli_log_dynamic_1 PGCGROWTHCONDITIONS
E.coli_log_dynamic_2 PGCGROWTHCONDITIONS
E.coli_log_dynamic_3 PGCGROWTHCONDITIONS
E.coli_log_rif_1 PGCGROWTHCONDITIONS
E.coli_log_rif_2 PGCGROWTHCONDITIONS
E.coli_log_rif_3 PGCGROWTHCONDITIONS
E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) PGCGROWTHCONDITIONS
E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation and harvested at stationary phase. (OD600nm ~ 1.5) PGCGROWTHCONDITIONS
E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation. For heat-shock, culture was mix with pre-warmed medium (50 °C) and incubated at 45 °C for 10 min. PGCGROWTHCONDITIONS
E. coli MG1655 strain was cultured in W2 minimal medium (for nitrogen-limiting condition) at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) (Powell, B. S. et al. J of Biol. Chem.270(9):4822) PGCGROWTHCONDITIONS
E.coli_nitrogen_dynamic_1 PGCGROWTHCONDITIONS
E.coli_nitrogen_dynamic_2 PGCGROWTHCONDITIONS
E.coli RNAP beta subunit ChIP DNA from heat-shocked condition without rifampicin treatment PGCGROWTHCONDITIONS
E.coli RNAP beta subunit ChIP DNA from mid-exponential condition without rifampicin treatment PGCGROWTHCONDITIONS
E.coli RNAP beta subunit ChIP DNA from mid-exponential condition with rifampicin treatment PGCGROWTHCONDITIONS
E.coli RNAP beta subunit ChIP DNA from nitrogen-limiting condition without rifampicin treatment PGCGROWTHCONDITIONS
E.coli RNAP beta subunit ChIP DNA from stationary condition without rifampicin treatment PGCGROWTHCONDITIONS
E.coli_stat_dynamic_1 PGCGROWTHCONDITIONS
E.coli_stat_dynamic_2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Input DNA from heat-shocked condition without rifampicin treatment PGCGROWTHCONDITIONS
Input DNA from mid-exponential condition without rifampicin treatment PGCGROWTHCONDITIONS
Input DNA from mid-exponential condition with rifampicin treatment PGCGROWTHCONDITIONS
Input DNA from nitrogen-limiting condition without rifampicin treatment PGCGROWTHCONDITIONS
Input DNA from stationary condition without rifampicin treatment PGCGROWTHCONDITIONS
reference: Input DNA PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
test: ChIP DNA PGCGROWTHCONDITIONS
The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP PGCGROWTHCONDITIONS
5 ml of the culture was mixed with 1 PGCGROWTHCONDITIONS
bovine-biased-1 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
bovine-biased-2 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
bovine-biased-3 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
bovine-biased-4 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
clinical-1 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
Clinical-1 vs Bovine-biased-1 PGCGROWTHCONDITIONS
Clinical-1 vs Bovine-biased-2 PGCGROWTHCONDITIONS
Clinical-1 vs Bovine-biased-3 PGCGROWTHCONDITIONS
Clinical-1 vs Bovine-biased-4 PGCGROWTHCONDITIONS
clinical-2 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
Clinical-2 vs Bovine-biased-1 PGCGROWTHCONDITIONS
Clinical-2 vs Bovine-biased-2 PGCGROWTHCONDITIONS
Clinical-2 vs Bovine-biased-3 PGCGROWTHCONDITIONS
Clinical-2 vs Bovine-biased-4 PGCGROWTHCONDITIONS
clinical-3 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
Clinical-3 vs Bovine-biased-1 PGCGROWTHCONDITIONS
Clinical-3 vs Bovine-biased-2 PGCGROWTHCONDITIONS
Clinical-3 vs Bovine-biased-3 PGCGROWTHCONDITIONS
Clinical-3 vs Bovine-biased-4 PGCGROWTHCONDITIONS
clinical-4 strain grown to exponential phase of growth PGCGROWTHCONDITIONS
Clinical-4 vs Bovine-biased-1 PGCGROWTHCONDITIONS
Clinical-4 vs Bovine-biased-2 PGCGROWTHCONDITIONS
Clinical-4 vs Bovine-biased-3 PGCGROWTHCONDITIONS
Clinical-4 vs Bovine-biased-4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
replicate: 4 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10915 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10916 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10917 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10938 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10948 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10950 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10957 PGCGROWTHCONDITIONS
strain: e. coli o157 H7 strain TW10967 PGCGROWTHCONDITIONS
The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (clinical or bovine-biased)+ sample (biological replicate) + error. Significant differences in expression due to strain were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR). SAM provided by TMEV was also used for data analysis. PGCGROWTHCONDITIONS
The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain as fixed factor. The linear model tested was Y (intensity) = array + dye + strain (clinical or bovine-biased)+ sample (biological replicate) + error. Significant differences in expression due to strain were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR). SAM provided by TMEV was also used for data analysis. PGCGROWTHCONDITIONS
TW10915 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10916 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10917 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10938 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10948 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10950 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10957 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
TW10967 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C. PGCGROWTHCONDITIONS
Batch cultures of E. coli MG1655 were grown at 37°C with shaking in Luria-Bertani medium (0.1% Bacto Tryptone, 0.05% yeast extract, 0.05% NaCl). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For cross-linking, 30 mL of cells were mixed with 300 uL 1M sodium phosphates (pH 7.6) and 810 uL 37% formaldehyde. Cross-linking was quenched by addition of 2 mL 2M glycine. Protein-DNA complexes were isolated from cells grown to early (2.4 x 10^7 CFU PGCGROWTHCONDITIONS
Genomic DNA Extraction: Genomic DNA was extracted according to Current Protocols in Molecular Biology.  Protein-DNA complex isolation: Protein-DNA complexes were isolated by phenol extraction with 150 μL 10 mM Tris and 500 μL 25:24:1 phenol : chloroform : isoamyl alcohol.  A white disk was readily discernible at the aqueous PGCGROWTHCONDITIONS
genomic_ref1 PGCGROWTHCONDITIONS
genomic_ref2 PGCGROWTHCONDITIONS
genomic_ref3 PGCGROWTHCONDITIONS
genomic_ref4 PGCGROWTHCONDITIONS
genomic_ref5 PGCGROWTHCONDITIONS
genomic_ref6 PGCGROWTHCONDITIONS
IPOD_early_log_1 PGCGROWTHCONDITIONS
IPOD_early_log_2 PGCGROWTHCONDITIONS
IPOD_late_log_1 PGCGROWTHCONDITIONS
IPOD_late_log_2 PGCGROWTHCONDITIONS
IPOD_MDS42 PGCGROWTHCONDITIONS
MDS42 DNA isolated from early-phase DNA-protein complexes PGCGROWTHCONDITIONS
MG1655 DNA isolated from early-phase DNA-protein complexes PGCGROWTHCONDITIONS
MG1655 DNA isolated from late-phase DNA-protein complexes PGCGROWTHCONDITIONS
MG1655 genomic DNA PGCGROWTHCONDITIONS
MG1655 RNA PGCGROWTHCONDITIONS
RNA_1 PGCGROWTHCONDITIONS
RNA_2 PGCGROWTHCONDITIONS
strain: MDS42 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
We developed in-house computational and statistical analysis tools for use with the E. coli tiling array.  We used a previous study (Choe et al., 2005) as a model for perfect match adjustment on single arrays.  Analysis scripts were written in Perl, MatLab, and R to standardize the statistical manipulations across all data sets. The output file from the scanning process is a CEL file. The raw CEL data were used as the basis for the manuscript; no processed data are available. PGCGROWTHCONDITIONS
antibody: Monoclonal antibody for RNA polymerase Beta' subunit (NT73) PGCGROWTHCONDITIONS
antibody: Monoclonal antibody for RNA polymerase Beta subunit (W0002) PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown with vigorous shaking at 37 °C to mid-log (light scattering at 600 nm equivalent to 0.4 OD). Sodium phosphate (1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA control from E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
Genomic DNA control from E. coli K-12 MG1655 cells, untreated PGCGROWTHCONDITIONS
reference: input Genomic DNA control PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells (Dataset 100040) PGCGROWTHCONDITIONS
RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells (Dataset 3427302) PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
RNA polymerase (Beta) ChIP in E. coli K-12 MG1655 cells treated with 20ug PGCGROWTHCONDITIONS
RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells, untreated PGCGROWTHCONDITIONS
RNA polymerase (Beta) ChIP in E. coli K-12 MG1655 cells, untreated PGCGROWTHCONDITIONS
Strain MG1655 cells were grown in MOPS minimal medium supplemented with 0.2% glucose (www.genome.wisc.edu PGCGROWTHCONDITIONS
The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. PGCGROWTHCONDITIONS
VALUE=log2(Cy5_signal PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 1 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 2 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 3 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 4 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 5 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 6 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 7 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 8 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 9 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 EDL933 Outside Control PGCGROWTHCONDITIONS
growth condition: Inside Acanthamoeba PGCGROWTHCONDITIONS
growth condition: Outside Control PGCGROWTHCONDITIONS
Mixed model analysis was conducted as previously described (Madsen, et al., 2006) excluding slide region and slide-by-region interaction effects. The value column was not used for analysis or in publication. The normalized values for duplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples. [mean log transformed median centered lowess normalized signal intensity] PGCGROWTHCONDITIONS
RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). Prior to lysis all samples were incubated for 30 min on ice in RNA stop solution (0.1% SDS, 1% Acidic phenol, 19% ethanol, ice cold). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR. PGCGROWTHCONDITIONS
BRP Induction 10 Minutes against 5 Minutes PGCGROWTHCONDITIONS
BRP Induction -10 minutes against 60 minutes PGCGROWTHCONDITIONS
BRP Induction 20 minutes against 10 minutes PGCGROWTHCONDITIONS
BRP Induction 30 minutes against 20 minutes PGCGROWTHCONDITIONS
BRP Induction 45 minutes against 30 minutes PGCGROWTHCONDITIONS
BRP Induction 5 minutes against 2 minutes PGCGROWTHCONDITIONS
BRP Induction 60 minutes against 45 minutes PGCGROWTHCONDITIONS
E.coli 0 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli -10 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 10 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 20 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 2 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 30 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 45 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 5 minutes after BRP induction PGCGROWTHCONDITIONS
E.coli 60 minutes after BRP induction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic response analysis of E.coli during coexpression of a bacteriocin release protein PGCGROWTHCONDITIONS
The scanning process of the hybridized chips included a fourteen-fold scan of each chip at different settings, altering both PMT and laser power settings. The following primary analysis served as a quantification method and is performed with the Gene Pix Pro 6.0™ (Molecular Devices, Sunnyvale, USA) software tool.  PGCGROWTHCONDITIONS
The secondary analysis is subsequently conducted using the data from the primary analysis. Therefore, data from different scans is first searched for saturation effects, which are eliminated. A locally weighted linear regression (Lowess) has been employed as a normalization method in order to account for intensity-dependent effects. Due to the lacking gene replicates on the commercial whole genome array, a t-test could not be applied. Instead, the quotients of respectively two states have been calculated for the assessment of the regulation. A absolute value of log-ratio (to base2) higher than 1 is used as criteria for a regulated gene. PGCGROWTHCONDITIONS
The strain was cultivated in 5L defined medium with glycerol as carbon source in a 7L (total) MBR-bioreactor. When the OD at 600 nm reached a value of around 5, the BAD – promoter was induced by adding 1g per litre and OD arabinose to the medium. Samples were taken at –10, 0, 2, 5, 10, 20, 30, 45 and 60 minutes related to point of induction. PGCGROWTHCONDITIONS
time point: 0 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: -10 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 10 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 20 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 2 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 30 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 45 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 5 minutes related to point of BRP induction PGCGROWTHCONDITIONS
time point: 60 minutes related to point of BRP induction PGCGROWTHCONDITIONS
Total RNA is extracted from 10^9 cells by phenol-chloroform extraction according to Sambrook et al. and ethanol precipitation with 5M NaCl. Subsequently a DNAse I digest at 37°C for 30 minutes and an additional phenol-chloroform extraction step is performed. Integrity of the total RNA is electrophoretically confirmed using the Agilent 2100 Bioanalyzer.  PGCGROWTHCONDITIONS
Total RNA is extracted from 10^9 cells by phenol-chloroform extraction and ethanol precipitation with 5M NaCl. Subsequently a DNAse I digest at 37°C for 30 minutes and an additional phenol-chloroform extraction step is performed. Integrity of the total RNA is electrophoretically confirmed using the Agilent 2100 Bioanalyzer.  PGCGROWTHCONDITIONS
0 min, 0.8% butanol PGCGROWTHCONDITIONS
0min-1 PGCGROWTHCONDITIONS
0min-2 PGCGROWTHCONDITIONS
0min-3 PGCGROWTHCONDITIONS
0 min, unstressed PGCGROWTHCONDITIONS
195 min, 0.8% butanol PGCGROWTHCONDITIONS
195min-1 PGCGROWTHCONDITIONS
195min-2 PGCGROWTHCONDITIONS
195min-3 PGCGROWTHCONDITIONS
195 min, unstressed PGCGROWTHCONDITIONS
30 min, 0.8% butanol PGCGROWTHCONDITIONS
30min-1 PGCGROWTHCONDITIONS
30min-2 PGCGROWTHCONDITIONS
30min-3 PGCGROWTHCONDITIONS
30 min, unstressed PGCGROWTHCONDITIONS
80 min, 0.8% butanol PGCGROWTHCONDITIONS
80min-1 PGCGROWTHCONDITIONS
80min-2 PGCGROWTHCONDITIONS
80min-3 PGCGROWTHCONDITIONS
80 min, unstressed PGCGROWTHCONDITIONS
Biomass was snap frozen in liquid nitrogen and stored at -80 C prior to extraction with Qiagen RNeasy Midi kits.  RNA integrity was verified with a 2100 Bioanalyzer (Agilent). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Feature fluorescence intensities [F532 media-B532 and F635media-B635] were extracted using GenePix Pro 6.0.  Local hybridization and intensity-dependent artifacts were removed with Lowess normalization using Standardization and Normalization of Microarray Data (SNOMAD, http: PGCGROWTHCONDITIONS
Individual clones of E. coli DH1 were grown in M9 MOPS media in 300 mL media in 1 L baffled flasks PGCGROWTHCONDITIONS
strain: E. coli DH1 PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
time: 195 min PGCGROWTHCONDITIONS
time: 30 min PGCGROWTHCONDITIONS
time: 80 min PGCGROWTHCONDITIONS
treatment: 0.8% n-butanol was added at time 0 PGCGROWTHCONDITIONS
81-4420 PGCGROWTHCONDITIONS
83-2315 PGCGROWTHCONDITIONS
86-1390 PGCGROWTHCONDITIONS
86-4220 PGCGROWTHCONDITIONS
87-4725 PGCGROWTHCONDITIONS
88-1861 PGCGROWTHCONDITIONS
88-4299 PGCGROWTHCONDITIONS
89-56-196 PGCGROWTHCONDITIONS
91-19-172 PGCGROWTHCONDITIONS
Data obtained from E. coli O157:H7 microarrays were normalized using the Ratio-based and Lowess methods in Acuity 3.1 (Axon instruments) before analysis. The normalized data for all strains were converted into log2 (Fluor 647 PGCGROWTHCONDITIONS
EDL (O157:H7) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. Sakai PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Overnight bacterial culture in BHI broth. PGCGROWTHCONDITIONS
referece: The three genomes contributing to the ORFs on the microarray. PGCGROWTHCONDITIONS
Sakai (O157:H7) PGCGROWTHCONDITIONS
See the paper Variation in the Genomic islands of porcine enteropathogenic Escherichia coli strains of serogroup O45 revealed by comparative genomic hybridization and PCR by Bruant and Zhang et al. 2009 PGCGROWTHCONDITIONS
strain: EHEC strain PGCGROWTHCONDITIONS
strain: Porcine EPEC strain O45 PGCGROWTHCONDITIONS
strain: Rabbit EPEC strain O103 PGCGROWTHCONDITIONS
The cultures were centrifuged at 8000 rpm for 10 minutes and the pellet was dissolved in 15 mL of 10 mM NaCl, 20 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 μg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FRIK2000 Cy3 rep1 vs EDL933 pool Cy5 PGCGROWTHCONDITIONS
FRIK2000 Cy3 rep3 vs EDL933 pool Cy5 PGCGROWTHCONDITIONS
FRIK2000 Cy5 rep2 vs EDL933 pool Cy3 PGCGROWTHCONDITIONS
FRIK2000 Cy5 rep4 vs EDL933 pool Cy3 PGCGROWTHCONDITIONS
FRIK966 Cy3 rep1 vs EDL933 pool Cy5 PGCGROWTHCONDITIONS
FRIK966 Cy3 rep3 vs EDL933 pool Cy5 PGCGROWTHCONDITIONS
FRIK966 Cy5 rep2 vs EDL933 pool Cy3 PGCGROWTHCONDITIONS
FRIK966 Cy5 rep4 vs EDL933 pool Cy3 PGCGROWTHCONDITIONS
isolate: bovine isolate of e coli o157: H7 FRIK2000 lineage II PGCGROWTHCONDITIONS
isolate: bovine isolate of e coli o157: H7 FRIK966 lineage II PGCGROWTHCONDITIONS
isolate: clinical isolate e coli o157: H7 lineage I PGCGROWTHCONDITIONS
late log phase grown e coli 966 into RNAprotect solution, RNA extracted with qiagen RNA bacteria kits PGCGROWTHCONDITIONS
late log phase grown e coli EDL933 into RNAprotect solution, RNA extracted with qiagen RNA bacteria kits PGCGROWTHCONDITIONS
Microarray data analyses were performed using Acuity 4.0 software. Slides were normalized using standard ratio-based methods. Data were analyzed based upon Log ratio (635 PGCGROWTHCONDITIONS
RNA from late log phase E coli EDL933 pooled reference PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK2000 rep 1 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK2000 rep 2 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK2000 rep 3 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK2000 rep 4 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK966 rep 1 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK966 rep 2 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK966 rep 3 PGCGROWTHCONDITIONS
RNA from late log phase E coli FRIK966 rep 4 PGCGROWTHCONDITIONS
strain: EDL933 PGCGROWTHCONDITIONS
strain: FRIK2000 PGCGROWTHCONDITIONS
strain: FRIK966 PGCGROWTHCONDITIONS
e.coli , 37°C, 60min PGCGROWTHCONDITIONS
E.coli, 37°C, 60min PGCGROWTHCONDITIONS
E.coli,37°C, 60min PGCGROWTHCONDITIONS
E.coli，37°C，60min  PGCGROWTHCONDITIONS
e.coli , 43°C, 60min PGCGROWTHCONDITIONS
E.coli, 43°C, 60min PGCGROWTHCONDITIONS
E.coli,43°C, 60min PGCGROWTHCONDITIONS
E.coli，43°C，60min  PGCGROWTHCONDITIONS
E. coli heat shock gene expression data using direct labeling method (replicate-1) PGCGROWTHCONDITIONS
E. coli heat shock gene expression data using direct labeling method (replicate-2) PGCGROWTHCONDITIONS
E. coli heat shock gene expression data using PAOD method (replicate-1) PGCGROWTHCONDITIONS
E. coli heat shock gene expression data using PAOD method (replicate-2) PGCGROWTHCONDITIONS
E. coli heat shock gene expression data using random priming method (replicate-1) PGCGROWTHCONDITIONS
E. coli heat shock gene expression data using random priming method (replicate-2) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
strain: DH5α PGCGROWTHCONDITIONS
The raw data were normalized using a space and intensity-dependant LOWESS program. Data from faint spots were removed, in which the intensity was lower than the average intensity plus 2 standard deviations of the negative controls on the array. For each experimental and control sample, amplification and hybridization were performed by a dye-swap strategy in two independent experiments. Differentially expressed genes were identified with at least 2 fold changes and q<0.001 criteria using SAM software . PGCGROWTHCONDITIONS
Total RNA was isolated from E.coli cells using NucleoSpin® RNA II kit according to the manufacturers’ instructions (Macherey Nagel, Duren, Germany). RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray and RT-PCR verification PGCGROWTHCONDITIONS
Total RNA was isolated from E.coli cells using NucleoSpin® RNA II kit according to the manufacturers’ instructions (Macherey Nagel, Duren, Germany). RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray and RT-PCR verification. PGCGROWTHCONDITIONS
DNA detected with GyrA immunoglobulin PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 1 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 2 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 3 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 4 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 5 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 6 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 7 PGCGROWTHCONDITIONS
gyrase binding (ChIP-chip) no. 8 PGCGROWTHCONDITIONS
Reference Genomic DNA PGCGROWTHCONDITIONS
Acidic Hot Phenol PGCGROWTHCONDITIONS
Cells were grown in Luria Bertani (LB) media at 37C at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at OD600 = 0.3 in exponential phase and at OD600 = 1.5 in stationary phase. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Exponential phase culture of EDL933 rpoS mutants in LB at OD600 of 0.3 PGCGROWTHCONDITIONS
Exponential phase culture of EDL933 wild type in LB at OD600 of 0.3 PGCGROWTHCONDITIONS
Exp-rpoS-rep1 PGCGROWTHCONDITIONS
Exp-rpoS-rep2 PGCGROWTHCONDITIONS
Exp-rpoS-rep3 PGCGROWTHCONDITIONS
Exp-WT-rep1 PGCGROWTHCONDITIONS
Exp-WT-rep2 PGCGROWTHCONDITIONS
Exp-WT-rep3 PGCGROWTHCONDITIONS
GCRMA method PGCGROWTHCONDITIONS
genotype: rpoS PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
growth phase: Exponential PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Stationary phase culture of EDL933 rpoS mutants in LB at OD600 of 1.5 PGCGROWTHCONDITIONS
Stationary phase culture of EDL933 wild type in LB at OD600 of 1.5 PGCGROWTHCONDITIONS
Stat-rpoS-rep1 PGCGROWTHCONDITIONS
Stat-rpoS-rep2 PGCGROWTHCONDITIONS
Stat-rpoS-rep3 PGCGROWTHCONDITIONS
Stat-WT-rep1 PGCGROWTHCONDITIONS
Stat-WT-rep2 PGCGROWTHCONDITIONS
Stat-WT-rep3 PGCGROWTHCONDITIONS
agent: no triclosan PGCGROWTHCONDITIONS
agent: triclosan PGCGROWTHCONDITIONS
E. coli imp fabI(G93V) [control] PGCGROWTHCONDITIONS
E. coli imp fabI(G94V) [control] PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
imp mutation: contains a 23 codon deletion allele in imp (increased membrane permeability),substitution of the 93th codon of fabI, NTG treatment; fabI(G93V), substitution of Gly(the 93th codon) of fabI with Val, NTG treatment to be high resistance to triclosan PGCGROWTHCONDITIONS
imp mutation: contains a 23 codon deletion allele in imp (increased membrane permeability),substitution of the 94th codon of fabI, NTG treatment; fabI(G93V), substitution of Gly(the 94th codon) of fabI with Val, NTG treatment to be high resistance to triclosan PGCGROWTHCONDITIONS
imp mutation: contains a 23 codon detion allele in imp (increased membrane permeability),substitution of the 93th codon of fabI; fabI(G93V), substitution of Gly(the 93th codon) of fabI with Val PGCGROWTHCONDITIONS
imp mutation: contains a 23 codon detion allele in imp (increased membrane permeability),substitution of the 94th codon of fabI; fabI(G93V), substitution of Gly(the 94th codon) of fabI with Val PGCGROWTHCONDITIONS
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal PGCGROWTHCONDITIONS
No triclosan treatment PGCGROWTHCONDITIONS
NTG-treated E. coli imp fabI(G93V) [E. coli IFN4] PGCGROWTHCONDITIONS
NTG-treated E. coli imp fabI(G93V) [E. coli IFN5] PGCGROWTHCONDITIONS
ntg treatment: yes PGCGROWTHCONDITIONS
passage: 4 PGCGROWTHCONDITIONS
strain: E. coli imp 4231(G93V) PGCGROWTHCONDITIONS
strain: E. coli imp 4231(G93V), substitution of the 93th codon of fabI PGCGROWTHCONDITIONS
strain: E. coli imp 4231(G93V), substitution of the 94th codon of fabI PGCGROWTHCONDITIONS
The cells were cultivated in 100 ml LB broth containing 2 mg PGCGROWTHCONDITIONS
Total RNA extracted using RNAprotect Bacterial Reagent (Qiagen) and an RNeasy Mini kit (Qiagen). PGCGROWTHCONDITIONS
Transcription profiles of NTG-treated E. coli imp fabI(G93V) and its control strain in the absence of triclosan PGCGROWTHCONDITIONS
Transcription profiles of NTG-treated E. coli imp fabI(G93V) and its control strain in the presence of triclosan PGCGROWTHCONDITIONS
Treatment of sub-lethal triclosan; 50 mg PGCGROWTHCONDITIONS
5mL of culture was mixed with 5mL of hot acid phenol:chloroform. Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1 PGCGROWTHCONDITIONS
EcJR-8 grown to OD600 = 0.5 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM). PGCGROWTHCONDITIONS
EcJR-8 grown to OD600 = 1.8 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM). PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. Sakai PGCGROWTHCONDITIONS
genotype: rpoN mutant (EcJR-8) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth protocol: logarithmic phase in DMEM-MOPS PGCGROWTHCONDITIONS
growth protocol: transition phase in DMEM-MOPS PGCGROWTHCONDITIONS
Logarithmic phase sample 1 PGCGROWTHCONDITIONS
Logarithmic phase sample 2 PGCGROWTHCONDITIONS
Logarithmic phase sample 3 PGCGROWTHCONDITIONS
Logarithmic phase sample 4 PGCGROWTHCONDITIONS
rpoN mutant grown to logarithmic phase PGCGROWTHCONDITIONS
rpoN mutant grown to transition phase PGCGROWTHCONDITIONS
Sakai grown to OD600 = 1.8 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM). PGCGROWTHCONDITIONS
The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain and growth phase as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (wild type or mutant) + growth phase (exponential or stationary) + strain*growth phase + sample (biological replicate) + error. Significant differences in expression due to strain, growth phase and strain*growth phase were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR). PGCGROWTHCONDITIONS
Transition phase sample 1 PGCGROWTHCONDITIONS
Transition phase sample 2 PGCGROWTHCONDITIONS
Transition phase sample 3 PGCGROWTHCONDITIONS
Transition phase sample 4 PGCGROWTHCONDITIONS
wild type grown to logarithmic phase PGCGROWTHCONDITIONS
wild type grown to transition phase PGCGROWTHCONDITIONS
E. coli, 1-h, serine hydroxamate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fifteen mL fermentation broth was used for each RNA extraction. Harvested cells were rapidly cooled in a -80°C ethanol bath, then centrifuged at 5000 g for seven minutes at 4°C. The supernatant was discarded. The cell pellet was frozen at -80°C. Thawed (on ice) cell pellets were suspended in 150 mL of TE buffer (10 mM Tris-HCl, pH 7.6, 0.1 mM EDTA) containing 0.75 mg PGCGROWTHCONDITIONS
Microarray suit 5.0 (Affymetrix Inc.) was used to average the scans and process the data, further data analysis was conducted using Affymetrix® Data Mining Tool (DMT 3.0). PGCGROWTHCONDITIONS
One set of fermentations were exposed to 5 mM IPTG and one set was not exposed to IPTG.  Samples were taken 0, 1, and 4 hours post-synchronization (Time S0, S1, and S4). PGCGROWTHCONDITIONS
plasmid: pPROEx-CAT PGCGROWTHCONDITIONS
Recombinant, high cell density, Time 0, no IPTG PGCGROWTHCONDITIONS
Recombinant, high cell density, Time 1 h, 5 mM IPTG PGCGROWTHCONDITIONS
Recombinant, high cell density, Time 1 h, no IPTG PGCGROWTHCONDITIONS
Recombinant, high cell density, Time 4 h, no IPTG PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S0, no IPTG, 1 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S0, no IPTG, 2 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S0, no IPTG, 3 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S1, IPTG, 1 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S1, IPTG, 2 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S1, IPTG, 3 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S1, no IPTG, 1 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S1, no IPTG, 2 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S1, no IPTG, 3 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S4, no IPTG, 1 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S4, no IPTG, 2 PGCGROWTHCONDITIONS
Recombinant, high cell density, Time S4, no IPTG, 3 PGCGROWTHCONDITIONS
Serine Hydroxamate stressed, replicate #1 PGCGROWTHCONDITIONS
Serine Hydroxamate stressed, replicate #2 PGCGROWTHCONDITIONS
Serine Hydroxamate stressed, replicate #3 PGCGROWTHCONDITIONS
Serine hydrxamate (100 mg PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The strain Escherichia coli MG1655 [pPROEx-CAT] was cultured in a fed-batch fermenter in LB media w PGCGROWTHCONDITIONS
The strain MG1655 [pPROEx-CAT] was cultured in a fed-batch fermenter in LB media w PGCGROWTHCONDITIONS
1A 1y PGCGROWTHCONDITIONS
1A 4y PGCGROWTHCONDITIONS
1A T0 PGCGROWTHCONDITIONS
2A 1y PGCGROWTHCONDITIONS
2A 4y PGCGROWTHCONDITIONS
3A 1m PGCGROWTHCONDITIONS
3A 1y PGCGROWTHCONDITIONS
3A 4y PGCGROWTHCONDITIONS
4A 1m PGCGROWTHCONDITIONS
4A 1y PGCGROWTHCONDITIONS
4A 4y PGCGROWTHCONDITIONS
5A 1m PGCGROWTHCONDITIONS
6A 1m PGCGROWTHCONDITIONS
9A 3y PGCGROWTHCONDITIONS
9A 5y PGCGROWTHCONDITIONS
9A T0 PGCGROWTHCONDITIONS
Alert PGCGROWTHCONDITIONS
Archaea PGCGROWTHCONDITIONS
Bacteria PGCGROWTHCONDITIONS
Bio1 1m PGCGROWTHCONDITIONS
Bio1 1y PGCGROWTHCONDITIONS
Bio2 1m PGCGROWTHCONDITIONS
Bio2 1y PGCGROWTHCONDITIONS
Bio3 1m PGCGROWTHCONDITIONS
Bio3 1y PGCGROWTHCONDITIONS
Bio4 1m PGCGROWTHCONDITIONS
Bio4 1y PGCGROWTHCONDITIONS
Bio-6 PGCGROWTHCONDITIONS
Bio Contro PGCGROWTHCONDITIONS
bioremediation treatment: Alert (ex situ) PGCGROWTHCONDITIONS
bioremediation treatment: Eureka (in situ) PGCGROWTHCONDITIONS
BZNT PGCGROWTHCONDITIONS
CompA PGCGROWTHCONDITIONS
CompB PGCGROWTHCONDITIONS
contamination status: hydrocarbon contaminated PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Eureka PGCGROWTHCONDITIONS
Lambda phage PGCGROWTHCONDITIONS
NFNT PGCGROWTHCONDITIONS
phage: Lambda PGCGROWTHCONDITIONS
Poly PGCGROWTHCONDITIONS
sample: 1A PGCGROWTHCONDITIONS
sample: 23S PGCGROWTHCONDITIONS
sample: 2A PGCGROWTHCONDITIONS
sample: 32D PGCGROWTHCONDITIONS
sample: 33D PGCGROWTHCONDITIONS
sample: 35B PGCGROWTHCONDITIONS
sample: 3A PGCGROWTHCONDITIONS
sample: 4A PGCGROWTHCONDITIONS
sample: 5A PGCGROWTHCONDITIONS
sample: #6 PGCGROWTHCONDITIONS
sample: 6A PGCGROWTHCONDITIONS
sample: 9A PGCGROWTHCONDITIONS
sample: Bio-1 PGCGROWTHCONDITIONS
sample: Bio-2 PGCGROWTHCONDITIONS
sample: Bio-3 PGCGROWTHCONDITIONS
sample: Bio-4 PGCGROWTHCONDITIONS
sample: Biopile control PGCGROWTHCONDITIONS
sample: BZ-NT PGCGROWTHCONDITIONS
sample: Composite A PGCGROWTHCONDITIONS
sample: Composite B PGCGROWTHCONDITIONS
sample: LC-1 PGCGROWTHCONDITIONS
sample: NC PGCGROWTHCONDITIONS
sample: NF-NT PGCGROWTHCONDITIONS
sample: Polygons PGCGROWTHCONDITIONS
sample: Vegetated PGCGROWTHCONDITIONS
Soil DNA was extracted from a 0.5g soil sub-sample using the MoBio DNA Power Soil kit (MoBio Laboratories, Carlsbad, CA). PGCGROWTHCONDITIONS
The intensity of each spot was measured with ScanArray Express using the histogram quantitation method; the percentile ranges for histograms were 80% for low signal range, 95% for high signal range, 5% for low background range and 20% for high background range. The median intensity minus the median background intensity was used for further calculations performed in Microsoft Excel. The background measurement refers to the local spot background intensity. Prior to normalization, all spots with a Signal-to-Noise ratio (SNR) lower than 3 were removed. The SNR was calculated using the following formula: (Median Signal – Median Background) PGCGROWTHCONDITIONS
year: 2000 PGCGROWTHCONDITIONS
year: 2001 PGCGROWTHCONDITIONS
year: 2003 PGCGROWTHCONDITIONS
year: 2004 PGCGROWTHCONDITIONS
year: 2005 PGCGROWTHCONDITIONS
year: 2006 PGCGROWTHCONDITIONS
year: 2007 PGCGROWTHCONDITIONS
year: 2008 PGCGROWTHCONDITIONS
0.5% (w PGCGROWTHCONDITIONS
0% sodiumbenzoate_0min PGCGROWTHCONDITIONS
0% sodiumbenzoate_15min PGCGROWTHCONDITIONS
0% sodiumbenzoate_30min PGCGROWTHCONDITIONS
0% sodiumbenzoate_5min PGCGROWTHCONDITIONS
0% sodiumbenzoate_60min PGCGROWTHCONDITIONS
Affymetrix Microarray Suite PGCGROWTHCONDITIONS
Cells were incubated at 37C prior to extraction PGCGROWTHCONDITIONS
E.coliO157_0.5% (w PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_0min_rep1 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_0min_rep2 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_15min_rep1 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_15min_rep2 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_30min_rep1 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_30min_rep2 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_5min_rep1 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_5min_rep2 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_60min_rep1 PGCGROWTHCONDITIONS
E.coliO157_0%sodiumbenzoate_60min_rep2 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
growth phase: stationary PGCGROWTHCONDITIONS
One hundred µl tris-EDTA buffer (10 mM Tris-Cl, 1 mM EDTA, ph 8.0; Promega; Madison, WI) containing lysozyme (3 mg PGCGROWTHCONDITIONS
Stationary phase growth (24hr) ~8 log CFU PGCGROWTHCONDITIONS
The RNeasy Mini Purification Kit (Qiagen; Valencia, CA) was used to extract total RNA from E. coli O157:H7 cultures.  RNAlater Stabilization Reagent (1.2 ml) (Qiagen; Valencia, CA) was combined with 0.6 ml E. coli O157:H7.  After 10 min at room temperature, the mixture was centrifuged at 8000 x g for 10 min under refrigeration.  The supernatant was decanted and the bacterial pellet was stored at -70°C until further processed (2-10 h). PGCGROWTHCONDITIONS
0.5 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
1.5 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
1 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
2 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
3.5 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
3 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
4 hour expression of synthetic protein DX in E. coli PGCGROWTHCONDITIONS
According to Invitrogen PureLink Micro-to-Midi Total RNA Purification System PGCGROWTHCONDITIONS
Data was processed by MATLAB to median normalize each channel and lowess normalize the sample set. PGCGROWTHCONDITIONS
E. coli cells containing a pBAD18 vector encoding synthetic protein DX exposed to arabinose inducer for 0.5h.  RNA extracted with Invitrogen PureLink kit. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Identical to Channel 1 with no arabinose added PGCGROWTHCONDITIONS
reference: E. coli TOP10 containing pBAD18 vector with no arabinose added PGCGROWTHCONDITIONS
RNA from E. coli 0.5 hours after inoculation PGCGROWTHCONDITIONS
RNA from E. coli 1.5 hours after inoculation PGCGROWTHCONDITIONS
RNA from E. coli 2 hours after inoculation PGCGROWTHCONDITIONS
RNA from E. coli 3.5 hours after inoculation PGCGROWTHCONDITIONS
RNA from E. coli 3 hours after inoculation PGCGROWTHCONDITIONS
RNA from E. coli 4 hours after inoculation PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 0.5 hours PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 1.5 hours PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 1 hours PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 2 hours PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 3.5 hours PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 3 hours PGCGROWTHCONDITIONS
RNA from E. coli expressing synthetic protein DX for 4 hours PGCGROWTHCONDITIONS
test: E. coli TOP10 containing pBAD18 vector exposed to arabinose inducer PGCGROWTHCONDITIONS
cell type: biofilm PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
growth protocol: biofilm grown on glass wool, 37C PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
medium: LB PGCGROWTHCONDITIONS
pCA24N-hns biofilm PGCGROWTHCONDITIONS
pCA24N-hnsK57N biofilm PGCGROWTHCONDITIONS
strain: BW25113 hha hns  PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
time: 7 hours PGCGROWTHCONDITIONS
Adapted E. coli (DST160, tolerant to high succinic acid concentration) PGCGROWTHCONDITIONS
E. coli W3110 (control) PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. W3110 PGCGROWTHCONDITIONS
High succinic acid tolerance E.coli_rep Dn PGCGROWTHCONDITIONS
High succinic acid tolerance E.coli_rep Up PGCGROWTHCONDITIONS
sample type: control PGCGROWTHCONDITIONS
sample type: test PGCGROWTHCONDITIONS
Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios. Logged gene expression ratios were normalized by LOWESS regression (Yang et al., 2002) using the GeneSpring GX 7.3 software (Agilent Technologies). PGCGROWTHCONDITIONS
The medium for continuous culture contained 3 g glucose medium consisted with 0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4•2H2O, 3 g KH2PO4 with separately added trace element of 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine per liter and the concentraiton of added succinate gradually was raised from 30 g PGCGROWTHCONDITIONS
The medium for continuous culture contained 3 g glucose medium consisted with 0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4•2H2O, 3 g KH2PO4 with separately added trace element of 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine per liter.  The fermentor was maintained at 37℃, 350 rpm with air gas flushing and the feeding and outlet pumps were maintained at flow rate of 0.1 h-1. PGCGROWTHCONDITIONS
The medium for continuous culture contained 3 g glucose medium consisted with 0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4•2H2O, 3 g KH2PO4 with separately added trace element of 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine per liter.  The fermentor was maintained at 37℃, 350 rpm with air gas flushing and the feeding and outlet pumps were maintained at flow rate of 0.1 h-1.  PGCGROWTHCONDITIONS
Transcriptome of cells was prepared using a RNA extraction kit (RNeasy mini kit;Qiagen, Hilden, Germany) PGCGROWTHCONDITIONS
Biofilms were grown on nylon membranes using agar as the source of nutrients and water.  Aliquots of 10 ml Luria agar were transferred to petri dishes to produce layers of agar approximately 3 mm in depth.  Nylon membrane filters (47 mm diameter) with a 0.2 μm pore size (Whatman) were autoclaved in Milli-Q water, dried and placed on the agar surface.  A 100 μl aliquot of an overnight culture (approximately 108 cells) was applied to the membrane as a single spot and allowed to dry.  All of these steps were performed on a level table so as not to introduce unwanted gradients.  Dishes were then inverted and incubated at 37 oC for 24 h. PGCGROWTHCONDITIONS
Biofilms were individually removed from the incubator and, using a small scalpel blade and sterile forceps, the distinctive outer perimeter of biofilm growth was cut away from the rest of the biofilm.  The two resulting sections of membrane were submerged in separate volumes of RNAprotect Bacteria Reagent and vortexed to release the cells.  The sections of membrane were then removed from the resulting suspension before RNA extraction. PGCGROWTHCONDITIONS
Cells were harvested by centrifugation at 5,000 g for 5 min.  Total RNA was purified using the RNeasy Mini kit (Qiagen) according to the supplier’s protocol (the composition of the RNeasy solutions are unknown).  The supernatant was decanted and 200 μl of TE buffer (10 mM Tris, 1 mM EDTA in DEPC-treated water, pH 8) plus lysosyme (Sigma) was used to resuspend the pellet.  This was mixed vigorously and incubated with intermittent shaking for 5 min at room temperature.  Buffer RLT (700 μl) with β-mercaptoethanol (10 μl of 14.3 M β-mercaptoethanol per 1 ml RTL) was then added to the solution.  The lysate was then mixed with 500 μl of absolute ethanol before applying the solution to an RNeasy Mini column.  This was then centrifuged for 15 s at 8,000 x g.  Buffer RW1 (700 μl) was applied to the column and centrifuged to wash the RNA.  At this point an RNase-free DNase on-column digest (Qiagen) was carried out, before the wash process was repeated twice with 500 μl of RPE buffer.  The RNA was eluted twice in one 30 μl volume of RNase-free water and stored at -70 oC. PGCGROWTHCONDITIONS
Colony Biofilm Replicate 1 PGCGROWTHCONDITIONS
Colony Biofilm Replicate 2 PGCGROWTHCONDITIONS
Colony Biofilm Replicate 3 PGCGROWTHCONDITIONS
Colony Biofilm Replicate 4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli Colony Biofilm Interior PGCGROWTHCONDITIONS
Escherichia coli Colony Biofilm Perimeter PGCGROWTHCONDITIONS
strain: TG-1 PGCGROWTHCONDITIONS
strain: TG-2 PGCGROWTHCONDITIONS
The average fluorescent signal intensity and local background correction for each spot were obtained using commercially available software from Biodiscovery Inc (Imagene, version 4.0 and Genesight, version 3.5).  Spots with a signal intensity lower than the background signal or those with blemishes were omitted from subsequent analysis.  The mean values from each channel were then log2 transformed and normalised using the LOWESS method to remove intensity-dependent effects in the log2 (ratios) values.  The Cy3 PGCGROWTHCONDITIONS
A-stat gene expression changes 0.3 PGCGROWTHCONDITIONS
A-stat gene expression changes 0.47 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli K12 MG1655 were grown in M9 minimal medium with 10 g PGCGROWTHCONDITIONS
specific growth rate: 0.3 h-1 PGCGROWTHCONDITIONS
Specific growth rate 0.3 h-1 PGCGROWTHCONDITIONS
specific growth rate: 0.47 h-1 PGCGROWTHCONDITIONS
Specific growth rate 0.47 h-1 PGCGROWTHCONDITIONS
Spot intensities and corresponding background signals were quantified with Genepix Pro (version 6; Axon Instruments [http: PGCGROWTHCONDITIONS
strain: Escherichia coli K12 MG1655 PGCGROWTHCONDITIONS
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA) and the genomic DNA was removed using RNase-Free DNase Set (QIAGEN). PGCGROWTHCONDITIONS
After collecting 50 ml culture as ‘non crosslinked’ sample, the rest of the cells was crosslinked.Crosslinked and non crosslinked cells were washed and sonicated. 400 µl of the sonicated extracts were mixed with 400 µl TE buffer and incubated with 2 µl RNase A (20 mg PGCGROWTHCONDITIONS
Cells were grown at 37 °C to an OD600 of about 0.15 in 100 ml LB (+ 0.2% glucose). PGCGROWTHCONDITIONS
Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking. PGCGROWTHCONDITIONS
Cells were grown in 65 ml LB medium at 30 °C to an OD600 of about 0.3. Subsequently 30 ml of culture were transformed to a pre warmed flask at 43 °C and the remainder kept at 30 °C (see control sample). PGCGROWTHCONDITIONS
Cells were grown in 65 ml LB medium at 30 °C to an OD600 of about 0.3. Subsequently 30 ml of culture were transformed to a pre warmed flask at 43 °C (see heat sample) and the remainder kept at 30 °C. PGCGROWTHCONDITIONS
chip antibody: none PGCGROWTHCONDITIONS
chip antibody: RNA polymerase subunit β PGCGROWTHCONDITIONS
chip antibody: SeqA PGCGROWTHCONDITIONS
chip antibody: σ32 PGCGROWTHCONDITIONS
Crosslink PGCGROWTHCONDITIONS
Crosslinked PGCGROWTHCONDITIONS
Cultures of E. coli MG1655 and its derivates were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected by centrifugation and washed twice with cold TBS (pH7.5). After resuspension in 1 ml lysis buffer (10mM Tris (pH 8.0), 20% sucrose, 50mM NaCl, 10mM EDTA, 10 mg PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
fraction: input DNA PGCGROWTHCONDITIONS
fraction: input DNA, SeqA ChIP supernatant PGCGROWTHCONDITIONS
fraction: input DNA, σ32 ChIP supernatant PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
genotype: ΔseqA PGCGROWTHCONDITIONS
Input DNA from E. Coli MG1655 PGCGROWTHCONDITIONS
Input DNA from E. Coli MG1655 ΔseqA PGCGROWTHCONDITIONS
Input DNA from SeqA ChIP supernatant PGCGROWTHCONDITIONS
Input DNA from ΔseqA-SeqA ChIP supernatant PGCGROWTHCONDITIONS
Input DNA from σ32 ChIP supernatant PGCGROWTHCONDITIONS
Non-crosslinked DNA PGCGROWTHCONDITIONS
RNAP ChIP DNA, old protocol PGCGROWTHCONDITIONS
RNAP old rep1 PGCGROWTHCONDITIONS
RNAP old rep2 PGCGROWTHCONDITIONS
SeqA ChIP DNA, new protocol PGCGROWTHCONDITIONS
SeqA ChIP DNA, old protocol PGCGROWTHCONDITIONS
SeqA new deltaSeqA PGCGROWTHCONDITIONS
SeqA new rep1 PGCGROWTHCONDITIONS
SeqA new rep2 PGCGROWTHCONDITIONS
SeqA old deltaSeqA PGCGROWTHCONDITIONS
SeqA old rep1 PGCGROWTHCONDITIONS
SeqA old rep2 PGCGROWTHCONDITIONS
Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction and normalized to the array wide average. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
strain: MG1655 ΔseqA PGCGROWTHCONDITIONS
σ32 30°C rep1 PGCGROWTHCONDITIONS
σ32 30°C rep2 PGCGROWTHCONDITIONS
σ32 30°C short RNase PGCGROWTHCONDITIONS
σ32 43°C rep1 PGCGROWTHCONDITIONS
σ32 43°C rep2 PGCGROWTHCONDITIONS
σ32 43°C short RNase PGCGROWTHCONDITIONS
σ32 ChIP DNA, control PGCGROWTHCONDITIONS
σ32 ChIP DNA, heat PGCGROWTHCONDITIONS
σ32 ChIP DNA, short RNase digestion PGCGROWTHCONDITIONS
At OD600~0.3, serine hydroxamate was added to a final concentration of 0.5mg PGCGROWTHCONDITIONS
Cells were grown in M9 medium supplemented with 0.2% glucose and 0.4% casamino acid at 37℃ PGCGROWTHCONDITIONS
Delta dksA Cells PGCGROWTHCONDITIONS
Delta dksA Cells Replicate 1 PGCGROWTHCONDITIONS
Delta dksA Cells Replicate 2 PGCGROWTHCONDITIONS
Delta dksA Cells Replicate 3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
GenePix Pro (v 6.1) was used for background subtraction and normalization. PGCGROWTHCONDITIONS
growth stage: log phase PGCGROWTHCONDITIONS
pooled reference RNA PGCGROWTHCONDITIONS
RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions. PGCGROWTHCONDITIONS
SHX-treated Delta dksA Cells PGCGROWTHCONDITIONS
SHX-treated Delta dksA Cells Replicate 1 PGCGROWTHCONDITIONS
SHX-treated Delta dksA Cells Replicate 2 PGCGROWTHCONDITIONS
SHX-treated Delta dksA Cells Replicate 3 PGCGROWTHCONDITIONS
SHX-treated Wild-type Cells PGCGROWTHCONDITIONS
SHX-treated Wild-type Cells Replicate 1 PGCGROWTHCONDITIONS
SHX-treated Wild-type Cells Replicate 2 PGCGROWTHCONDITIONS
SHX-treated Wild-type Cells Replicate 3 PGCGROWTHCONDITIONS
strain: MG1655 delta lac PGCGROWTHCONDITIONS
strain: MG1655 delta lac delta dksA PGCGROWTHCONDITIONS
strain: MG1655 delta lac + MG1655 delta lac delta dksA PGCGROWTHCONDITIONS
treatment: 0.5mg PGCGROWTHCONDITIONS
treatment: No treatment PGCGROWTHCONDITIONS
treatment: Pooled RNA from mixture of the same amount of wt, wt+SHX, dksA, dksA+SHX RNA samples PGCGROWTHCONDITIONS
Wild-type Cells PGCGROWTHCONDITIONS
Wild-type Cells Replicate 1 PGCGROWTHCONDITIONS
Wild-type Cells Replicate 2 PGCGROWTHCONDITIONS
Wild-type Cells Replicate 3 PGCGROWTHCONDITIONS
Biotinylated GST protein PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GSH-sepharose 4b purification PGCGROWTHCONDITIONS
GST control Protoarray replicate 1 PGCGROWTHCONDITIONS
protein: GST expressed in E. coli BL21(DE3) from pGEX-4T-3 PGCGROWTHCONDITIONS
purification: Protein purified using GSH-sepharose 4b (GE Life Sciences) PGCGROWTHCONDITIONS
Scanned spot signals were normalized using internal Protoarray control proteins and Z scores subsequently determined based on comparisons of mean signals for each spot pair to the mean spot intensity for the array. Z scores greater than 3.0 were considered significant PGCGROWTHCONDITIONS
After the final wash & staining step, Affymetrix GeneChip® E.coli Genome array was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software. The raw .cel file generated through above procedure meant expression intensity data and was used for the next step. PGCGROWTHCONDITIONS
EDL 933 at 37oC at OD 1.0 PGCGROWTHCONDITIONS
EDL 933 with 0.1 mg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Expression data were normalized using the Affymetrix microarray suite 5(MAS5) algorithm implemented in Affymetrix expression console software .  To reduce noise for the significance analysis, probe sets that did not show detection call rate at least 50% of the samples in the comparison were filtered out. Highly expressed genes that showed a 2-fold change in expression were selected.  PGCGROWTHCONDITIONS
(http: PGCGROWTHCONDITIONS
strain: EDL 933 PGCGROWTHCONDITIONS
The web-based tool, DAVID (the Database for Annotation, Visualization, and Integrated Discovery) was used to perform the biological interpretation of differentially expressed genes. Then, these genes were classified based on the information of gene function in Gene ontology database.  PGCGROWTHCONDITIONS
Total RNA was isolated using Ribopure Bacteria Kit as described by the manufacturer (Ambion, Huntingdon, UK). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA). PGCGROWTHCONDITIONS
Cells harvested at mid-exponential phase, spun, washed twice with M9 medium and shifted to limiting or no thymine medium. Samples taken at listed intervals. PGCGROWTHCONDITIONS
E. coli - 0 min before nutrient shift PGCGROWTHCONDITIONS
E. coli - 15 min after shift to limiting medium PGCGROWTHCONDITIONS
E. coli - 15 min after shift to thymineless medium PGCGROWTHCONDITIONS
E. coli - 30 min after shift to limiting medium PGCGROWTHCONDITIONS
E. coli - 30 min after shift to thymineless medium PGCGROWTHCONDITIONS
E. coli - 45 min after shift to limiting medium PGCGROWTHCONDITIONS
E. coli - 45 min after shift to thymineless medium PGCGROWTHCONDITIONS
E. coli - 60 min after shift to limiting medium PGCGROWTHCONDITIONS
E. coli - 60 min after shift to thymineless medium PGCGROWTHCONDITIONS
E. coli - 90 min after shift to limiting medium PGCGROWTHCONDITIONS
E. coli - 90 min after shift to thymineless medium PGCGROWTHCONDITIONS
E. coli MG1655 thyA- cells grown in M9 minimal medium + 0.2% glucose and 20 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Lowess normalized data. Resultant data is log2 normalized. PGCGROWTHCONDITIONS
strain: MG1655 thyA- PGCGROWTHCONDITIONS
TLD-15-rep1 PGCGROWTHCONDITIONS
TLD-15-rep2 PGCGROWTHCONDITIONS
TLD-30-rep1 PGCGROWTHCONDITIONS
TLD-30-rep2 PGCGROWTHCONDITIONS
TLD-45-rep1 PGCGROWTHCONDITIONS
TLD-45-rep2 PGCGROWTHCONDITIONS
TLD-60-rep1 PGCGROWTHCONDITIONS
TLD-60-rep2 PGCGROWTHCONDITIONS
TLD-90-rep1 PGCGROWTHCONDITIONS
TLD-90-rep2 PGCGROWTHCONDITIONS
TLM-15 PGCGROWTHCONDITIONS
TLM-30 PGCGROWTHCONDITIONS
TLM-45 PGCGROWTHCONDITIONS
TLM-60 PGCGROWTHCONDITIONS
TLM-90 PGCGROWTHCONDITIONS
Total RNA extracted using QIAGEN RNeasy kit according to manufacturer's instructions PGCGROWTHCONDITIONS
Channel 1 PGCGROWTHCONDITIONS
E. coli O157:H7 86-24 in LB at 37oC at OD 4.0 PGCGROWTHCONDITIONS
E. coli O157:H7 86-24 was inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 250 rpm and 37°C for an absorbance of 4.0 at 600 nm.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC at OD 4.0 PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 was inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 250 rpm and 37°C for an absorbance of 4.0 at 600 nm.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
strain: 86-24 PGCGROWTHCONDITIONS
strain: EDL933 PGCGROWTHCONDITIONS
All cultures were grown aerobically in a thermostatically controlled 37oC culture room. Cultures (150ml culture volume) were stirred by magnetic stirrers at 330 rpm (Thermo Scientific Variomag Multipoint 6in) 1000ml Erlenmeyer flask. Starting cultures were inoculated from a single colony and grown overnight. Each experimental culture was then inoculated from such an overnight culture at a dilution of 1:20 into 150 ml fresh MOPS minimal medium in a 1000 ml flask. The minimal medium used for all experiments was a modification of MOPS (morpholinopropane sulfonate) minimal medium obtained from Teknova, CA (product number M2006) which contains 86 mM NaCl, 9.5 mM NH4Cl, 5 mM K2HPO4 and 0.2% glucose. PGCGROWTHCONDITIONS
coli_coldstress_timepoint1_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint1_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint1_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint2_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint2_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint2_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint3_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint3_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint3_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint4_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint4_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint4_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint5_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint5_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint5_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint6_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint6_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint6_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint7_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint7_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint7_rep3 PGCGROWTHCONDITIONS
coli_coldstress_timepoint8_rep1 PGCGROWTHCONDITIONS
coli_coldstress_timepoint8_rep2 PGCGROWTHCONDITIONS
coli_coldstress_timepoint8_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint1_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint1_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint1_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint2_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint2_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint2_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint3_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint3_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint3_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint4_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint4_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint4_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint5_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint5_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint5_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint6_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint6_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint6_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint7_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint7_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint7_rep3 PGCGROWTHCONDITIONS
coli_control_timepoint8_rep1 PGCGROWTHCONDITIONS
coli_control_timepoint8_rep2 PGCGROWTHCONDITIONS
coli_control_timepoint8_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint1_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint1_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint1_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint2_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint2_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint2_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint3_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint3_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint3_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint4_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint4_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint4_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint5_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint5_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint5_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint6_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint6_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint6_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint7_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint7_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint7_rep3 PGCGROWTHCONDITIONS
coli_heatstress_timepoint8_rep1 PGCGROWTHCONDITIONS
coli_heatstress_timepoint8_rep2 PGCGROWTHCONDITIONS
coli_heatstress_timepoint8_rep3 PGCGROWTHCONDITIONS
coli_lactose_timepoint2_rep1 PGCGROWTHCONDITIONS
coli_lactose_timepoint2_rep2 PGCGROWTHCONDITIONS
coli_lactose_timepoint2_rep3 PGCGROWTHCONDITIONS
coli_lactose_timepoint3_rep1 PGCGROWTHCONDITIONS
coli_lactose_timepoint3_rep3 PGCGROWTHCONDITIONS
coli_lactose_timepoint4_rep1 PGCGROWTHCONDITIONS
coli_lactose_timepoint4_rep2 PGCGROWTHCONDITIONS
coli_lactose_timepoint4_rep3 PGCGROWTHCONDITIONS
coli_lactose_timepoint5_rep1 PGCGROWTHCONDITIONS
coli_lactose_timepoint5_rep2 PGCGROWTHCONDITIONS
coli_lactose_timepoint5_rep3 PGCGROWTHCONDITIONS
coli_lactose_timepoint6_rep1 PGCGROWTHCONDITIONS
coli_lactose_timepoint6_rep2 PGCGROWTHCONDITIONS
coli_lactose_timepoint6_rep3 PGCGROWTHCONDITIONS
coli_lactose_timepoint7_rep1 PGCGROWTHCONDITIONS
coli_lactose_timepoint7_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint10_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint10_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint10_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint11_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint11_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint11_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint12_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint1_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint1_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint1_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint2_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint2_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint2_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint3_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint3_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint3_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint4_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint4_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint4_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint5_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint5_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint5_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint6_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint6_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint6_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint7_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint7_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint7_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint8_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint8_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint8_rep4 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint9_rep1 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint9_rep2 PGCGROWTHCONDITIONS
coli_oxidativestress_timepoint9_rep4 PGCGROWTHCONDITIONS
Escherichia coli_stress experiment PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For further analyses the processed signal intensities of all coding regions and RNA genes were extracted and used. Variance stabilization and normalization of the extracted intensities were performed with the vsn packages of the R software environment (R Development Core Team, 2007) and back-transformed to normal intensity scale. For each probeset, e.g. all probes representing for example, a single coding gene, outliers were removed by boxplot statistics and the outlier-removed probe intensities were averaged in a robust way by computing the Tukey biweight. PGCGROWTHCONDITIONS
Oxidative stress 200 ug PGCGROWTHCONDITIONS
RNA was extracted using the Qiagen RNeasy Mini Kit (74104) and mechanical cell disruption with glass beads but without enzymatic lysis. This was carried out in the Qiagen RNeasy kit lysis RLT buffer with beta-mercaptethanol, according to the manufacturer’s recommendations. Mechanical cell disruption was completed through shaking for five min using a Retsch mill (Retsch MM200) on maximum speed. RNA was subsequently cleaned on-column with an additional DNase treatment (Qiagen 79254). The quality of extracted RNA was determined with an Agilent 2100 bioanalyzer having used an Agilent RNA 6000 Nano Kit according to the manufacturer’s recommendations. PGCGROWTHCONDITIONS
treatment group: cold stress PGCGROWTHCONDITIONS
treatment group: control PGCGROWTHCONDITIONS
treatment group: heat stress PGCGROWTHCONDITIONS
treatment group: lactose shift PGCGROWTHCONDITIONS
treatment group: oxidative stress PGCGROWTHCONDITIONS
treatment time: T10: 210 min after stress PGCGROWTHCONDITIONS
treatment time: T11: 235 min after stress PGCGROWTHCONDITIONS
treatment time: T12: 260 min after stress PGCGROWTHCONDITIONS
treatment time: T1: OD 0.3 PGCGROWTHCONDITIONS
treatment time: T1: OD 0.5 PGCGROWTHCONDITIONS
treatment time: T2: OD 0.5 PGCGROWTHCONDITIONS
treatment time: T2: OD 0.6 PGCGROWTHCONDITIONS
treatment time: T3: 10 min after reaching OD 0.6 PGCGROWTHCONDITIONS
treatment time: T3: 10 min after stress PGCGROWTHCONDITIONS
treatment time: T3: OD 0.6 PGCGROWTHCONDITIONS
treatment time: T3: OD 0.7 PGCGROWTHCONDITIONS
treatment time: T4: 10 min after growth lag PGCGROWTHCONDITIONS
treatment time: T4: 10 min after stress PGCGROWTHCONDITIONS
treatment time: T4: 20 min after reaching OD 0.6 PGCGROWTHCONDITIONS
treatment time: T4: 20 min after stress PGCGROWTHCONDITIONS
treatment time: T5: 20 min after growth lag PGCGROWTHCONDITIONS
treatment time: T5: 20 min after stress PGCGROWTHCONDITIONS
treatment time: T5: 30 min after reaching OD 0.6 PGCGROWTHCONDITIONS
treatment time: T5: 30 min after stress PGCGROWTHCONDITIONS
treatment time: T6: 30 min after growth lag PGCGROWTHCONDITIONS
treatment time: T6: 30 min after stress PGCGROWTHCONDITIONS
treatment time: T6: 40 min after reaching OD 0.6 PGCGROWTHCONDITIONS
treatment time: T6: 40 min after stress PGCGROWTHCONDITIONS
treatment time: T7: 40 min after growth lag PGCGROWTHCONDITIONS
treatment time: T7: 40 min after stress PGCGROWTHCONDITIONS
treatment time: T7: 50 min after reaching OD 0.6 PGCGROWTHCONDITIONS
treatment time: T7: 50 min after stress PGCGROWTHCONDITIONS
treatment time: T8: 90 min after reaching OD 0.6 PGCGROWTHCONDITIONS
treatment time: T8: 90 min after stress PGCGROWTHCONDITIONS
treatment time: T9: 150 min after stress PGCGROWTHCONDITIONS
bile+1 PGCGROWTHCONDITIONS
bile+2 PGCGROWTHCONDITIONS
bile+3 PGCGROWTHCONDITIONS
ctrl1 PGCGROWTHCONDITIONS
ctrl2 PGCGROWTHCONDITIONS
ctrl3 PGCGROWTHCONDITIONS
E.coli O157:H7 in LB at mid-log phase PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
growth media: LB PGCGROWTHCONDITIONS
growth media: LB; 0.8% bile salts PGCGROWTHCONDITIONS
growth phase: mid-log phase PGCGROWTHCONDITIONS
Hot phenol extraction of total RNA. PGCGROWTHCONDITIONS
O157:H7 cells were grown to mid-log phase in Luria broth with or without 0.8% bile salts. PGCGROWTHCONDITIONS
strain: strain O157:H7 PGCGROWTHCONDITIONS
The data were imported into FlexArray using gc-RMA preprocessing for analysis. PGCGROWTHCONDITIONS
8 ml of the culture was mixed with 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
serotype: o157:H7 clade 2, stx 1 and 2 PGCGROWTHCONDITIONS
serotype: o157:H7 clade 2, stx 2 PGCGROWTHCONDITIONS
serotype: o157:H7 clade 8, stx 2 PGCGROWTHCONDITIONS
serotype: o157:H7 clade 8, stx 2 and 2c PGCGROWTHCONDITIONS
strains TW014359 vs TW04863 epithelial exposure PGCGROWTHCONDITIONS
strains TW014359 vs TW11037 epithelial exposure PGCGROWTHCONDITIONS
strains TW02883 vs TW11028 epithelial exposure PGCGROWTHCONDITIONS
strains TW04863 vs TW14279 epithelial exposure PGCGROWTHCONDITIONS
strains TW07591 vs TW09098 epithelial exposure PGCGROWTHCONDITIONS
strains TW07937 vs TW11185 epithelial exposure PGCGROWTHCONDITIONS
strains TW07961 vs TW08610 epithelial exposure PGCGROWTHCONDITIONS
strains TW07961 vs TW11029 epithelial exposure PGCGROWTHCONDITIONS
strains TW08030 vs TW10045 epithelial exposure PGCGROWTHCONDITIONS
strains TW08609 vs TW08030 epithelial exposure PGCGROWTHCONDITIONS
strains TW08609 vs TW08623 epithelial exposure PGCGROWTHCONDITIONS
strains TW08609 vs TW11110 epithelial exposure PGCGROWTHCONDITIONS
strains TW08610 vs TW11110 epithelial exposure PGCGROWTHCONDITIONS
strains TW08623 vs TW02883 epithelial exposure PGCGROWTHCONDITIONS
strains TW08623 vs TW08030 epithelial exposure PGCGROWTHCONDITIONS
strains TW08635 vs TW09098 epithelial exposure PGCGROWTHCONDITIONS
strains TW09098 vs TW11308 epithelial exposure PGCGROWTHCONDITIONS
strains TW09189 vs TW11032 epithelial exposure PGCGROWTHCONDITIONS
strains TW09189 vs TW14279 epithelial exposure PGCGROWTHCONDITIONS
strains TW10012 vs TW11037 epithelial exposure PGCGROWTHCONDITIONS
strains TW10012 vs TW14313 epithelial exposure PGCGROWTHCONDITIONS
strains TW10045 vs TW07937 epithelial exposure PGCGROWTHCONDITIONS
strains TW11028 vs TW07937 epithelial exposure PGCGROWTHCONDITIONS
strains TW11028 vs TW11308 epithelial exposure PGCGROWTHCONDITIONS
strains TW11029 vs TW02883 epithelial exposure PGCGROWTHCONDITIONS
strains TW11029 vs TW08610 epithelial exposure PGCGROWTHCONDITIONS
strains TW11032 vs TW04863 epithelial exposure PGCGROWTHCONDITIONS
strains TW11032 vs TW09189 epithelial exposure PGCGROWTHCONDITIONS
strains TW11037 vs TW08635 epithelial exposure PGCGROWTHCONDITIONS
strains TW11110 vs TW10012 epithelial exposure PGCGROWTHCONDITIONS
strains TW11185 vs TW014313 epithelial exposure PGCGROWTHCONDITIONS
strains TW11185 vs TW08635 epithelial exposure PGCGROWTHCONDITIONS
strains TW11308 vs TW07591 epithelial exposure PGCGROWTHCONDITIONS
strains TW14279 vs TW10045 epithelial exposure PGCGROWTHCONDITIONS
strains TW14313 vs TW07591 epithelial exposure PGCGROWTHCONDITIONS
strains TW14359 vs TW07961 epithelial exposure PGCGROWTHCONDITIONS
strain TW02883 PGCGROWTHCONDITIONS
strain TW02883  PGCGROWTHCONDITIONS
strain TW04863 PGCGROWTHCONDITIONS
strain TW07591 PGCGROWTHCONDITIONS
strain TW07937 PGCGROWTHCONDITIONS
strain TW07961 PGCGROWTHCONDITIONS
strain TW07961  PGCGROWTHCONDITIONS
strain TW08030 PGCGROWTHCONDITIONS
strain TW08609 PGCGROWTHCONDITIONS
strain TW08609  PGCGROWTHCONDITIONS
strain TW08610 PGCGROWTHCONDITIONS
strain TW08623 PGCGROWTHCONDITIONS
strain TW08635 PGCGROWTHCONDITIONS
strain TW08635  PGCGROWTHCONDITIONS
strain TW09098 PGCGROWTHCONDITIONS
strain TW09098  PGCGROWTHCONDITIONS
strain TW09189 PGCGROWTHCONDITIONS
strain TW10012 PGCGROWTHCONDITIONS
strain TW10045 PGCGROWTHCONDITIONS
strain TW10045  PGCGROWTHCONDITIONS
strain TW11028 PGCGROWTHCONDITIONS
strain TW11029 PGCGROWTHCONDITIONS
strain TW11029  PGCGROWTHCONDITIONS
strain TW11032 PGCGROWTHCONDITIONS
strain TW11032  PGCGROWTHCONDITIONS
strain TW11037 PGCGROWTHCONDITIONS
strain TW11110 PGCGROWTHCONDITIONS
strain TW11110  PGCGROWTHCONDITIONS
strain TW11185 PGCGROWTHCONDITIONS
strain TW11185  PGCGROWTHCONDITIONS
strain TW11308 PGCGROWTHCONDITIONS
strain TW11308  PGCGROWTHCONDITIONS
strain TW14279 PGCGROWTHCONDITIONS
strain TW14279  PGCGROWTHCONDITIONS
strain TW14313 PGCGROWTHCONDITIONS
strain TW14359 PGCGROWTHCONDITIONS
Thirty-six dye-swap hybridizations were performed between four groups with six strains per group, according to a balanced double loop design.  Strains were grouped based on cladestx profiles and each strain was considered an independent biological replicate of its group (n=6).  The six strains from each group were randomly hybridized with six strains from every other group; each hybridization compared a pair of strains that differed in either clade or stx profile, or both.  Subsequent to local Lowess normalization, averaging of replicate probes and log2 transformation,  the microarray data were fitted to a 2-factor mixed ANOVA model (intensity = Array + Dye + Clade + Stx + Clade:Stx + Sample; where the biological replicate (Sample) and array effects were considered random effects, while all other effects were considered fixed effects), using the MAANOVA package (version 0.98-8) in R software (version 2.2.1).  This model allows independent consideration of the effect of ‘Clade’ (clade divergence) and ‘Stx’ (stx type variation) parameters on differences in gene expression among O157:H7 strains, as well as their interaction (combined) effect (Clade:Stx).  Overall differences in gene expression between groups were determined using the Fs test, followed by pair-wise contrasts to determine significant differential expression between each pair of groups.  Subsequently, the Fs statistic was estimated for the ‘Clade’ effect to determine significant differences in gene expression between clades 8 (n=12) and 2 (n=12), regardless of stx profile.  Similarly, the Fs statistic was estimated for the ‘Stx’ effect as well as the ‘Clade:Stx’ interaction effect to examine the combined effect of clade and stx type on differences in gene expression among O157:H7 strains.  In other words, this analysis will determine whether the expression of any given gene among groups with different stx types is also dependent on clade.  An interaction effect would be observed if expression estimates between strain groups clade8stx2 and clade2stx2 are different from expression estimates between strain groups clade8stx2,2c and clade2stx1,2.  For every analysis, 1000 permutations of the data were performed to generate P values; estimates were considered significant if the P value was < 0.05 after adjusting for multiple comparisons.  PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
-Leu t=0 PGCGROWTHCONDITIONS
-Leu t=0 charged PGCGROWTHCONDITIONS
-Leu t=0 total PGCGROWTHCONDITIONS
-Leu t=17 PGCGROWTHCONDITIONS
-Leu t=17 charged PGCGROWTHCONDITIONS
-Leu t=17 total PGCGROWTHCONDITIONS
-Leu t=2 PGCGROWTHCONDITIONS
-Leu t=2 charged PGCGROWTHCONDITIONS
-Leu t=2 total PGCGROWTHCONDITIONS
-Leu t=32 PGCGROWTHCONDITIONS
-Leu t=32 charged PGCGROWTHCONDITIONS
-Leu t=32 total PGCGROWTHCONDITIONS
-Leu t=7 PGCGROWTHCONDITIONS
-Leu t=7 charged PGCGROWTHCONDITIONS
-Leu t=7 total PGCGROWTHCONDITIONS
Bear feces isolate B1 PGCGROWTHCONDITIONS
Bear feces isolate B3 PGCGROWTHCONDITIONS
Bear feces isolate B5 PGCGROWTHCONDITIONS
Bear III versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Bear III versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Bear II versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Bear II versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Bear I versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Bear I versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Cattle feces isolate C1A PGCGROWTHCONDITIONS
Cattle feces isolate C4A PGCGROWTHCONDITIONS
Cattle feces isolate C6D PGCGROWTHCONDITIONS
Cattle III versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Cattle III versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Cattle II versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Cattle II versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Cattle I versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Cattle I versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Deer feces isolate D1 PGCGROWTHCONDITIONS
Deer feces isolate D3 PGCGROWTHCONDITIONS
Deer feces isolate W6A PGCGROWTHCONDITIONS
Deer III versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Deer III versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Deer II versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Deer II versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Deer I versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Deer I versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genomic DNA was extracted using an SDS lysis PGCGROWTHCONDITIONS
Human III versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Human III versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Human II versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Human II versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Human I versus MG1655 technical replicate 1 PGCGROWTHCONDITIONS
Human I versus MG1655 technical replicate 2 PGCGROWTHCONDITIONS
Human sewage isolate H1 PGCGROWTHCONDITIONS
Human sewage isolate H2 PGCGROWTHCONDITIONS
Human sewage isolate H3 PGCGROWTHCONDITIONS
Images were analyzed using a combination of GenePix Pro 6.0, the freely available TIGR TM4 software suite (www.tm4.org ) and Microsoft Excel.  Spots with an intensity: background ratio > 1.5 and overall intensity > 350 in the reference channel and an intensity:background ratio of > 1.0 in the experimental channel were considered acceptable for downstream processing.  Local background was subtracted for each spot, the corresponding log2 ratios were normalized using total intensity normalization, and replicate spots were averaged using TIGR MIDAS.  Genes that had missing data (i.e. unacceptable spots) for more than one-third of the samples were excluded from the downstream analysis leaving 3993 ORFs in the final data set.  Each sample was hybridized twice and the results averaged in Microsoft Excel after processing with MIDAS.  A strict cutoff of log2 ratio > 0.9 or < 0.9 was applied for the determination of gene amplifications and gene absences, respectively. PGCGROWTHCONDITIONS
strain: Bear feces isolate B1 PGCGROWTHCONDITIONS
strain: Bear feces isolate B3 PGCGROWTHCONDITIONS
strain: Bear feces isolate B5 PGCGROWTHCONDITIONS
strain: Cattle feces isolate C1A PGCGROWTHCONDITIONS
strain: Cattle feces isolate C4A PGCGROWTHCONDITIONS
strain: Cattle feces isolate C6D PGCGROWTHCONDITIONS
strain: Deer feces isolate D1 PGCGROWTHCONDITIONS
strain: Deer feces isolate D3 PGCGROWTHCONDITIONS
strain: Deer feces isolate W6A PGCGROWTHCONDITIONS
strain: E. coli K12 MG1655 PGCGROWTHCONDITIONS
strain: Human sewage isolate H1 PGCGROWTHCONDITIONS
strain: Human sewage isolate H2 PGCGROWTHCONDITIONS
strain: Human sewage isolate H3 PGCGROWTHCONDITIONS
At time point 0, rifampicin was added to a final concentration of 500ug PGCGROWTHCONDITIONS
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from lysates by phenol PGCGROWTHCONDITIONS
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
strain: DY330 (W3110) PGCGROWTHCONDITIONS
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
time point 0 PGCGROWTHCONDITIONS
time point 2 PGCGROWTHCONDITIONS
time point 4 PGCGROWTHCONDITIONS
time point 6 PGCGROWTHCONDITIONS
time point 8 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 0 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 2 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 4 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 6 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 8 PGCGROWTHCONDITIONS
10min PGCGROWTHCONDITIONS
10min (additional) PGCGROWTHCONDITIONS
15min PGCGROWTHCONDITIONS
15min (additional) PGCGROWTHCONDITIONS
5min PGCGROWTHCONDITIONS
5min (additional) PGCGROWTHCONDITIONS
control PGCGROWTHCONDITIONS
control (additional) PGCGROWTHCONDITIONS
E. coli cell PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Cells grew in MOPS minimal medium with 0.4% glucose and 0.2 mM K2HPO4 and harvested at the OD600 value of 1.0. PGCGROWTHCONDITIONS
E. coli MG1655 PhoB knock-out strain grows under phosphate starvation condition PGCGROWTHCONDITIONS
E. coli MG1655 wildtype strain grows under phosphate starvation condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
PhoB knock-out strain, rep1 PGCGROWTHCONDITIONS
PhoB knock-out strain, rep2 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The data were normalized by RMA method and then analyzed by limma package to identify differentially expressed genes (bioconductor). PGCGROWTHCONDITIONS
Trizol extraction of total RNA was performed according to the manufacturer's instructions. PGCGROWTHCONDITIONS
Wildtype strain, rep1 PGCGROWTHCONDITIONS
wildtype strain, rep2 PGCGROWTHCONDITIONS
E4 -O2 1 PGCGROWTHCONDITIONS
E4 +O2 1 PGCGROWTHCONDITIONS
E4 -O2 2 PGCGROWTHCONDITIONS
E4 +O2 2 PGCGROWTHCONDITIONS
E4 -O2 3 PGCGROWTHCONDITIONS
E4 +O2 3 PGCGROWTHCONDITIONS
E. coli MG1655, M9 media with 4 g PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
No specific treatment was done. Samples were collected in the mid-log growth phase for expression analysis PGCGROWTHCONDITIONS
Respiratory defecient E. coli mutant (ECOM4), M9 media with 4 g PGCGROWTHCONDITIONS
strain: ECOM4 PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
The data were analyzed with ArrayStar 3 (DNASTAR) using RMA normalization method. Genes with at least two-fold expression level change and FDR-adjusted P-value (T-test) of less than 0.05 were considered significant. PGCGROWTHCONDITIONS
total RNA was extreacted using Quagen RNA mini kit. DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000. PGCGROWTHCONDITIONS
Wild type and the mutant were grown on minimal M9 media with 4 g PGCGROWTHCONDITIONS
WT -O2 1 PGCGROWTHCONDITIONS
WT +O2 1 PGCGROWTHCONDITIONS
WT -O2 2 PGCGROWTHCONDITIONS
WT +O2 2 PGCGROWTHCONDITIONS
WT -O2 3 PGCGROWTHCONDITIONS
WT +O2 3 PGCGROWTHCONDITIONS
Cells grew in MOPS minimal medium with 0.4% glucose and 0.2 mM K2HPO4 and harvested at the OD600 value of 1.0. PGCGROWTHCONDITIONS
ChIP DNA from MG1655_PhoB_FLAG PGCGROWTHCONDITIONS
ChIP DNA from MG1655 wild type strain PGCGROWTHCONDITIONS
Cultures were grown to the OD600 value of 1.0 and treated with 1% formaldehyde for 10 min. To quench the reaction, glycine was added at the final concentration of 0.125 M for 5 min. Cells were washed twice with lysis buffer (10 mM Tris-HCl (pH 7.4), 0.1 M NaCl, 1 mM EDTA and 0.5% Tween-20). The washed cells were then lysed with the lysis buffer containing 8 KU PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
PhoB_ChIP, rep1 PGCGROWTHCONDITIONS
PhoB_ChIP, rep2 PGCGROWTHCONDITIONS
PhoB_ChIP, rep3 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The R package, Ringo, was used to read the pair files and the limma package for within- and between-array normalization. ChIP-chip data were bi-weighted scaled within each array and aquantile normalized between arrays. PGCGROWTHCONDITIONS
0.15% Bile Salt Mix Stress, 90 minutes, static, 5% CO2 (EHEC strain: 86-24) PGCGROWTHCONDITIONS
Bacteria were grown in LB broth overnight and subcultured in DMEM to OD600 of 0.4. Bacteria were then spun down, media removed and repalced with DMEM.  PGCGROWTHCONDITIONS
Bacteria were grown in LB broth overnight and subcultured in DMEM to OD600 of 0.4. Bacteria were then spun down, media removed and repalced with DMEM plus 0.15% bile salt mix.  PGCGROWTHCONDITIONS
Bile salt stress was done in DMEM at pH 7.4 (unbuffered) at 37C, 5% CO2, static incubation for 90 minutes PGCGROWTHCONDITIONS
Control treatment. Bacteria were grown in DMEM pH 7.4, 90 minutes, 37C, 5% CO2, static (unstressed) PGCGROWTHCONDITIONS
Cy3 labeled EHEC grown in DMEM pH 7.4, 90 minutes PGCGROWTHCONDITIONS
Cy5 labeled EHEC bile salt-stressed in DMEM, 90 minutes PGCGROWTHCONDITIONS
ehec strain: 86-24 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) PGCGROWTHCONDITIONS
Signal intensities were averaged among the technical replicates.  Two types of data analysis were performed: to indentify density-dependent changes in gene expression, single averaged normalized signal intensities for each treatment point were compared to the average of corresponding unstressed control signal intensities.  Genes which showed a relative signal log2ratio (SLR) value above 1.0 or below -1.0 were selected for further analysis.  PGCGROWTHCONDITIONS
After quality controls of data distribution the raw data (CEL files) were used to perform, normalization and probe set summarization through RMA algorithm (Robust Multiarray Analysis) by using the Affymetrix Gene Expression Console Software (www.affymetrix.com).   Normalized data were then uploaded into OneChannelGUI Software (http: PGCGROWTHCONDITIONS
E.coli_IVT-RNA_sigma70-1 PGCGROWTHCONDITIONS
E.coli_IVT-RNA_sigma70-2 PGCGROWTHCONDITIONS
E.coli_IVT-RNA_sigmaS PGCGROWTHCONDITIONS
E.coli_IVT-RNA_sigmaS-2 PGCGROWTHCONDITIONS
E. coli RNA polymerase core enzyme was purchased from Epicentre (Madison, WI, USA). Histidine-tagged σ factors were produced and purified as described (Lacour et al., 2003; Checroun et al., 2004); proteins appeared pure from contaminants as determined by denaturing protein gel electrophoresis (data not shown). For reconstitution of RNA polymerase holoenzymes, the core enzyme was incubated for 10 minutes at 37 °C with either σS or σ70 at a 1:10 ratio. For calculation of RNA polymerase concentrations in transcription assays, it was assumed that, after reconstitution, core enzyme would be 100% active and fully saturated by either σ factor. 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI were used in transcription assays for ROMA experiments. RNA polymerase holoenzyme concentrations were 100 nM in 50 ul reaction mixture. Ten independent run-off transcription assays were performed, and transcripts were pooled together (ca. 1 ug total RNA). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
RNA produced by in vitro transcription, with RNA polymerase E σ70, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI PGCGROWTHCONDITIONS
RNA produced by in vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI PGCGROWTHCONDITIONS
sample type: cDNA produced by RT of RNA deriving from vitro transcription, with RNA polymerase E σ70, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI PGCGROWTHCONDITIONS
sample type: cDNA produced by RT of RNA deriving from vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI PGCGROWTHCONDITIONS
Cells in RNAlater were aliquoted into two. One served as non-sorted cells and kept at 4 degree C. The other aliquot was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater. PGCGROWTHCONDITIONS
Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). LOWESS normalization was performed with three iterations using a smoothing factor of 0.4. Hybridized spots having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3 PGCGROWTHCONDITIONS
E. coli cells were grown in annular reactor (BioSurface Technologies, Bozeman, MT) inoculated with 1 ml overnight cultures and supplied with fresh 10-fold diluted Luria broth at 100 ml PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
growth mode: planktonic culture in annular reactor PGCGROWTHCONDITIONS
growth time: 7-day PGCGROWTHCONDITIONS
non-sorted E. coli cells from culture 1 PGCGROWTHCONDITIONS
non-sorted E. coli cells from culture 2 PGCGROWTHCONDITIONS
RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS PGCGROWTHCONDITIONS
sorted E. coli cells from culture 1 PGCGROWTHCONDITIONS
sorted E. coli cells from culture 2 PGCGROWTHCONDITIONS
sorted vs. non-sorted cells bioreplicate 1 technical replicate 1 PGCGROWTHCONDITIONS
sorted vs. non-sorted cells bioreplicate 1 technical replicate 2 PGCGROWTHCONDITIONS
sorted vs. non-sorted cells bioreplicate 2 technical replicate 1 PGCGROWTHCONDITIONS
sorted vs. non-sorted cells bioreplicate 2 technical replicate 2 PGCGROWTHCONDITIONS
strain: K-12 PHL644 PGCGROWTHCONDITIONS
treatment: non-sorted PGCGROWTHCONDITIONS
treatment: sorted PGCGROWTHCONDITIONS
Bacteria were inoculated by direct injection of the mouse bladder, and kidney samples were taken at day 2 post-infection PGCGROWTHCONDITIONS
cDNA made from strain KMD extracted from mouse kidney on day 2 post infection PGCGROWTHCONDITIONS
cDNA made from strain PC1012(marArobsoxS) extracted from mouse kidney on day 2 post infection PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Infected kidney solutions were centrifuged at 5000xg for 10 min to separate bacteria (pellet) from kidney (surface of RNA-later solution) cells.  The kidney cells were evacuated from the top of the solution, and the remaining solution was spun once more at 12000xg for 10 min, followed by disposal of the supernatant.  Pelleted cells were resuspended in TE buffer and treated with lysozyme (Sigma) at 1mg PGCGROWTHCONDITIONS
KMD 1 PGCGROWTHCONDITIONS
KMD 2 PGCGROWTHCONDITIONS
KMD 3 PGCGROWTHCONDITIONS
Mouse kidneys were homogonized in RNALater solution (Ambion) and bacterial titers were taken.  Samples were pooled, and centrifuged as described below PGCGROWTHCONDITIONS
PC 1 PGCGROWTHCONDITIONS
PC 2 PGCGROWTHCONDITIONS
PC 3 PGCGROWTHCONDITIONS
strain: KMD PGCGROWTHCONDITIONS
strain: PC1012 PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. PGCGROWTHCONDITIONS
tissue source: kidney from CD-1 mice PGCGROWTHCONDITIONS
Cells aerobically grown to mid-log phase in MOPS PGCGROWTHCONDITIONS
Control PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample1_TechRep1 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample1_TechRep2 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample2_TechRep1 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample2_TechRep2 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample3_TechRep1 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample3_TechRep2 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample4_TechRep1 PGCGROWTHCONDITIONS
Ecoli_WT_100uM_KCN_Sample4_TechRep2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files. The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu PGCGROWTHCONDITIONS
RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column. PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Treated with 100 uM KCN for 5 minutes before harvesting PGCGROWTHCONDITIONS
Untreated PGCGROWTHCONDITIONS
Astat_chemostat PGCGROWTHCONDITIONS
A-stat, specific growth rate 0.48 1 PGCGROWTHCONDITIONS
chemostat, specific growth rate 0.51 1 PGCGROWTHCONDITIONS
cultivation: continuous cultivation, A-stat PGCGROWTHCONDITIONS
cultivation: continuous cultivation, chemostat PGCGROWTHCONDITIONS
eco_0.21_0.11 PGCGROWTHCONDITIONS
eco_0.26_0.11 PGCGROWTHCONDITIONS
eco_0.31_0.11 PGCGROWTHCONDITIONS
eco_0.36_0.11 PGCGROWTHCONDITIONS
eco_0.40_0.11 PGCGROWTHCONDITIONS
eco_0.48_0.11 PGCGROWTHCONDITIONS
Escherichia coli K12 MG1655 was cultivated using M9 minimal medium containing 4.5 g PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Image was analized with Genepix 6 pro followed by background substration and global LOWESS normalization in R environment (KTH package). Spots with signal to noise ratio lower that 3 and PGCGROWTHCONDITIONS
RNA degradation was stopped using Qiagen's RNAprotect reagent PGCGROWTHCONDITIONS
specific growth rate 0.11 1 PGCGROWTHCONDITIONS
specific growth rate 0.21 1 PGCGROWTHCONDITIONS
specific growth rate 0.26 1 PGCGROWTHCONDITIONS
specific growth rate 0.31 1 PGCGROWTHCONDITIONS
specific growth rate 0.36 1 PGCGROWTHCONDITIONS
specific growth rate 0.40 1 PGCGROWTHCONDITIONS
specific growth rate 0.48 1 PGCGROWTHCONDITIONS
Total RNA was extracted with Qiagen's Rneasy Mini Kit PGCGROWTHCONDITIONS
Bordetella sp. IITR-02 PGCGROWTHCONDITIONS
ECDH5_GD_RP1 PGCGROWTHCONDITIONS
Escherichia coli BL21 PGCGROWTHCONDITIONS
Escherichia coli DH5[alpha] PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genomic DNA of all strains (degraders and non-degraders) isolated individually and mixed in equal ratio (500ng each) PGCGROWTHCONDITIONS
Genomic DNA of Escherichia coli DH5α PGCGROWTHCONDITIONS
Genomic DNA of mixed culture containing only non-degraders in equal ratio PGCGROWTHCONDITIONS
Genomic DNA of mixed culture (Degraders and non-degraders in 2:1 ratio) PGCGROWTHCONDITIONS
Genomic DNA of mixed culture (Degraders: NM-05, IITR-02, RHA1; Non-degraders: DH5α, BL21 and K12 in equal ratio) PGCGROWTHCONDITIONS
Images were quantified using Agilent Feature Extraction Software (10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities. PGCGROWTHCONDITIONS
Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1 & 10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities. PGCGROWTHCONDITIONS
isolation source: Mixed culture PGCGROWTHCONDITIONS
isolation source: Pure culture PGCGROWTHCONDITIONS
MC_Val_G1 PGCGROWTHCONDITIONS
MC_Val_G2 PGCGROWTHCONDITIONS
MC_Val_G3 PGCGROWTHCONDITIONS
MC_Val_G5 PGCGROWTHCONDITIONS
Rhodococcus jostii RHA1 PGCGROWTHCONDITIONS
Sphingomonas sp. NM05 PGCGROWTHCONDITIONS
The genomic DNA from pure and mixed bacterial cultures was isolated using the Wizard genomic DNA isolation kit (Promega corporation, Madison, USA) as per manufacturer's instructions. The concentration of DNA was analyzed by Nanodrop spectrophotometer (Nanodrop Technologies Inc, Rockland, USA), and quality was determined by analysis on DNA 12000 kit (Caliper Sciences, USA) using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). PGCGROWTHCONDITIONS
The Sphingomonas sp. strain NM-05 used in the study is a known degrader of γ-hexachlorocyclohexane (γ-HCH) and has been isolated from the vicinity of an industry India Pesticide Limited, Chinhat industrial area, Lucknow which is involved in manufacturing chlorinated pesticides for last 25 years. The strain was harvested in mineral salt medium with 0.34mM γ-HCH as sole source of carbon and energy. The strain Bordetella sp. strain IITR-02 used in this study has been isolated from the vicinity of the industry India Pesticide Limited, Chinhat, Lucknow and is found to be a degrader of 1,2-, 1,4-dichloro and 1,2,3- and 1,2,4-trichlorobenzene. The strain was harvested in mineral salt medium with 3.2mM of 1,2,4-trichlorobenzene as sole source of carbon and energy. The bacterium Rhodococcus sp. strain RHA1 which is a known degrader of polychlorinated biphenyls, substituted phenols, benzoates and phthalates was grown on 0.2% biphenyl and 20mM of benzoate as carbon sources. The strain Escherichia coli DH5α and Escherichia coli BL21 were grown in Luria-Bertani medium and strain Escherichia coli K12  was grown in nutrient broth to an OD560nm of 0.4 at 37 degree centigrade with continuous shaking. PGCGROWTHCONDITIONS
The Sphingomonas sp. strain NM-05 used in the study is a known degrader of γ-hexachlorocyclohexane (γ-HCH) and has been isolated from the vicinity of an industry India Pesticide Limited, Chinhat industrial area, Lucknow which is involved in manufacturing chlorinated pesticides for last 25 years. The strain was harvested in mineral salt medium with 0.34mM γ-HCH as sole source of carbon and energy. The strain Escherichia coli DH-5α was grown in Luria-Bertani medium to an O.D. of 0.4 at 37 degree centigrade with continuous shaking. The soil PGCGROWTHCONDITIONS
The total DNA to be used as target for microarray hybridization was isolated from soil PGCGROWTHCONDITIONS
Data from two independent experiments were normalized and then analyzed using the GenePix Pro 3.0 software (Axon Instruments). PGCGROWTHCONDITIONS
Escherichia coli ptsN mutant strain PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli wild type strain PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
ptsN mutant replicate 1 PGCGROWTHCONDITIONS
ptsN mutant replicate 2 PGCGROWTHCONDITIONS
RNA was extracted from each sample using a QIAGEN RNA extraction kit according to the manufacturer’s instruction PGCGROWTHCONDITIONS
The E. coli K12 strain MG1655 and its isogenic ptsN mutant were grown in M9 minimal medium containing 0.5% glucose as carbon source. Cells from duplicate experiments were harvested in exponential growth phase when cultures reached an A600 of 0.4. PGCGROWTHCONDITIONS
Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculation and were inoculated into 5 ml 10% LB in a disposable petri dish (60 mm x 15 mm). 50 ul E. coli culture was inoculated for mono-species pure culture. 50 ul E. coli and 10 ul S. maltophilia were mixed and inoculated for mixed-species culture. Petri dishes were set static at room temperature (20 C) for 18 h for biofilm growth. PGCGROWTHCONDITIONS
culture media: 10% Luria broth PGCGROWTHCONDITIONS
culture system: static petri dish (disposable) PGCGROWTHCONDITIONS
culture temperature: room temperature (20 C) PGCGROWTHCONDITIONS
culture time: 18 h PGCGROWTHCONDITIONS
Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). Hybridized spots for E. coli K12 having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_1 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_2 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_3 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesBiofilm_bioreplicate2_techreplicate_1 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesBiofilm_bioreplicate2_techreplicate_2 PGCGROWTHCONDITIONS
RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS PGCGROWTHCONDITIONS
sorted E. coli cells from dual-species biofilms 1 PGCGROWTHCONDITIONS
sorted E. coli cells from dual-species biofilms 2 PGCGROWTHCONDITIONS
sorted E. coli cells from mono-species biofilms 1 PGCGROWTHCONDITIONS
sorted E. coli cells from mono-species biofilms 2 PGCGROWTHCONDITIONS
Suspended cells were then removed and biofilms were washed 3 times with 1 ml 10% LB broth. Biofilms from each petri dish were then scraped into a vial containing 1 ml 10% LB. Scraped biofilms in each vial were concentrated from 1 ml into 50 ul by centrifugation. 500 ul RNAlater was added and mixed well. Samples in RNAlater were kept in 4C fridge overnight.  Each vial was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extractions. PGCGROWTHCONDITIONS
treatment: with homogenization and separation PGCGROWTHCONDITIONS
Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculated into 30 ml 10% LB in a flask. 300 ul E. coli culture was inoculated for mono-species pure culture. 150 ul E. coli and 60 ul S. maltophilia were mixed and inoculated for mixed-species cultures. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h. PGCGROWTHCONDITIONS
Cells were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Cells were aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extraction. PGCGROWTHCONDITIONS
culture media: 10% Luria broth PGCGROWTHCONDITIONS
culture system: flask with continous shaking (250 rpm) PGCGROWTHCONDITIONS
culture system: flask with continuous shaking (250 rpm) PGCGROWTHCONDITIONS
culture temperature: room temperature (20 C) PGCGROWTHCONDITIONS
culture time: 18 h PGCGROWTHCONDITIONS
Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). Hybridized spots for E. coli K12 having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesPlanktonic_bioreplicate1_techreplicate_1 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesPlanktonic_bioreplicate1_techreplicate_2 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesPlanktonic_bioreplicate2_techreplicate_1 PGCGROWTHCONDITIONS
Escherichia coli_MixedSpeciesPlanktonic_bioreplicate2_techreplicate_2 PGCGROWTHCONDITIONS
RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS PGCGROWTHCONDITIONS
sorted E. coli cells from dual-species planktonic culture 1 PGCGROWTHCONDITIONS
sorted E. coli cells from dual-species planktonic culture 2 PGCGROWTHCONDITIONS
sorted E. coli cells from mono-species pure planktonic culture 1 PGCGROWTHCONDITIONS
sorted E. coli cells from mono-species pure planktonic culture 2 PGCGROWTHCONDITIONS
treatment: with homogenization and separation PGCGROWTHCONDITIONS
Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculation. Planktonic cultures were conducted in flasks with 30 ml 10% LB, inoculated with 300 ul E. coli overnight culture. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h. Biofilms were cultivated in static disposable petri dishes (60 mm x 15 mm) with 5 ml 10% LB, inoculated with 50 ul E. coli overnight culture. The petri dishes were set static at room temperature (20 C) for 18 h. PGCGROWTHCONDITIONS
culture media: 10% Luria broth PGCGROWTHCONDITIONS
culture system: flask with continuous shaking (250 rpm) PGCGROWTHCONDITIONS
culture system: static petri dish (disposable) PGCGROWTHCONDITIONS
culture temperature: room temperature (20 C) PGCGROWTHCONDITIONS
culture time: 18 h PGCGROWTHCONDITIONS
Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). Hybridized spots for E. coli K12 having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3 PGCGROWTHCONDITIONS
E. coli cells from biofilm 1 PGCGROWTHCONDITIONS
E. coli cells from biofilm 2 PGCGROWTHCONDITIONS
E. coli cells from planktonic culture 1 PGCGROWTHCONDITIONS
E. coli cells from planktonic culture 2 PGCGROWTHCONDITIONS
Escherichia coli_Biofilm_bioreplicate1_techreplicate_1 PGCGROWTHCONDITIONS
Escherichia coli_Biofilm_bioreplicate1_techreplicate_2 PGCGROWTHCONDITIONS
Escherichia coli_Biofilm_bioreplicate2_techreplicate_1 PGCGROWTHCONDITIONS
Escherichia coli_Biofilm_bioreplicate2_techreplicate_2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Planktonic cultures of E. coli were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Suspended cells were removed from petri dishes and biofilms were washed three times with fresh 10% LB before being craped from the bottom surface of petri dishes. Biofilms were also re-suspeded into RNAlater and kept at 4C overnight. Both planktonic and biofilm samples were homogenized for 2 min on ice with an Omni TH homogenizer. Cells were then aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater. PGCGROWTHCONDITIONS
RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS PGCGROWTHCONDITIONS
treatment: with homogenization and separation PGCGROWTHCONDITIONS
chip antibody: FLAG antibody PGCGROWTHCONDITIONS
chip antibody: RNAP beta subunit antibody PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
[E-MTAB-332] fis early-exponential PGCGROWTHCONDITIONS
[E-MTAB-332] fis mid-exponential PGCGROWTHCONDITIONS
[E-MTAB-332] H-NS early-exponential PGCGROWTHCONDITIONS
[E-MTAB-332] H-NS mid-exponential PGCGROWTHCONDITIONS
[E-MTAB-332] H-NS stationary PGCGROWTHCONDITIONS
[E-MTAB-332] H-NS transition-to-stationary PGCGROWTHCONDITIONS
[E-MTAB-332] rpo delfis mid-exponential PGCGROWTHCONDITIONS
[E-MTAB-332] rpo delhns mid-exponential PGCGROWTHCONDITIONS
[E-MTAB-332] rpo wt mid-exponential PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fis, EE PGCGROWTHCONDITIONS
Fis, ME PGCGROWTHCONDITIONS
genotype: del-fis PGCGROWTHCONDITIONS
genotype: del-hns PGCGROWTHCONDITIONS
genotype: fis::3xFLAG PGCGROWTHCONDITIONS
genotype: hns::3xFLAG PGCGROWTHCONDITIONS
genotype: wild_type PGCGROWTHCONDITIONS
growth condition: early-exponential PGCGROWTHCONDITIONS
growth condition: mid-exponential PGCGROWTHCONDITIONS
growth condition: stationary PGCGROWTHCONDITIONS
growth condition: transition-to-stationary PGCGROWTHCONDITIONS
grow | The E. coli K-12 MG1655 bacterial strains used in this work are the following: E. coli MG1655 (F- lambda- ilvG- rfb-50 rph-1); MG1655 hns (hns::Kanr); MG1655 fis (fis::Kanr); MG1655 hns-FLAG (hns::3xFLAG::Kanr); MG1655 fis-FLAG (fis::3xFLAG::Kanr). Luria-Bertani (0.5% NaCl) broth and agar (15 g PGCGROWTHCONDITIONS
H-NS, EE PGCGROWTHCONDITIONS
H-NS, ME PGCGROWTHCONDITIONS
H-NS, S PGCGROWTHCONDITIONS
H-NS, TS PGCGROWTHCONDITIONS
material type: whole_organism PGCGROWTHCONDITIONS
nucleic_acid_extraction | ChIP was performed as previously described (Grainger et al, 2004) with some modifications to the protdegree Col. Cells were grown aerobically at 37degree C to the desired OD600 and formaldehyde was added to a final concentration of 1%. After 20 min of incubation, glycine was added to a final concentration of 0.5 M to quench the reaction and incubated for a further 5 min. Cross-linked cells were harvested by centrifugation and washed twice with ice-cold TBS (pH 7.5). Cells were resuspended in 1 ml of lysis buffer (10 mM Tris [pH 8.0], 20% sucrose, 50 mM NaCl, 10 mM EDTA, 20 mg PGCGROWTHCONDITIONS
rpo, delfis, ME PGCGROWTHCONDITIONS
rpo, delhns, ME PGCGROWTHCONDITIONS
rpo, wt, ME PGCGROWTHCONDITIONS
Sequences obtained from the Illumina Genome Analyzer were mapped to both strands of the E. coli K12 MG1655 genome using BLAT allowing no gaps and up to two mismatches. Each alignment was extended to 200bp the approximate average length of DNA fragments on the 3' end. Only reads which mapped to a single region of the genome were considered for further analysis. For each base position on the genome, the number of reads that mapped to that position was calculated. PGCGROWTHCONDITIONS
sequencing| Immunoprecipitated samples and the sheared DNA following the Bioruptor were de-crosslinked in 0.5x elution buffer containing 0.8 mg PGCGROWTHCONDITIONS
strainorline: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Cells were grown at 37oC without shaking in 18 mm test tubes containing 5 ml of the MOPS-based culture medium designed by Neidhardt. Mouse cecal mucus was prepared from streptomycin-treated CD-1 mice (not colonized with E. coli). Cultures were grown to A600 = 0.4 in MOPS medium containing glucose or mannose (0.2%) and also in 10 mg PGCGROWTHCONDITIONS
Cultures were diluted into DNA-RNA Protect (Sierra Diagnostics) to inhibit RNA degradation and the RNA was purified using RNeasy minkits with the optional DNase treatment (Qiagen). PGCGROWTHCONDITIONS
E. coli flhD, A600=0.2 on mucus PGCGROWTHCONDITIONS
E. coli flhD, A600=0.4 on glucose PGCGROWTHCONDITIONS
E. coli flhD, A600=0.4 on mannose PGCGROWTHCONDITIONS
E. coli flhD, A600=0.5 on mucus PGCGROWTHCONDITIONS
E. coli MG1655star, A600=0.2 on mucus PGCGROWTHCONDITIONS
E. coli MG1655star, A600=0.4 on glucose PGCGROWTHCONDITIONS
E. coli MG1655star, A600=0.4 on mannose PGCGROWTHCONDITIONS
E. coli MG1655star, A600=0.5 on mucus PGCGROWTHCONDITIONS
E. coli wild-type, A600=0.2 on mucus PGCGROWTHCONDITIONS
E. coli wild-type, A600=0.4 on glucose PGCGROWTHCONDITIONS
E. coli wild-type, A600=0.4 on mannose PGCGROWTHCONDITIONS
E. coli wild-type, A600=0.5 on mucus PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
flhD-glucose PGCGROWTHCONDITIONS
flhD-mannose PGCGROWTHCONDITIONS
flhD-mucus-P1 PGCGROWTHCONDITIONS
flhD-mucus-P2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
MG1655star-glucose PGCGROWTHCONDITIONS
MG1655star-mannose PGCGROWTHCONDITIONS
MG1655star-mucus-P1 PGCGROWTHCONDITIONS
MG1655star-mucus-P2 PGCGROWTHCONDITIONS
RMA with quartile normalization according to method of Irizarry et al, 2003. The raw .cel files were processed in RMA using Bioconductor R package: affy Version:1.8.1 Date:2005-09-03, with the option Filter.genes containing a subset of probesets corresponding to MG1655 genes and intergenic regions listed in the matrix data. Replicates were averaged for ratio calculations. PGCGROWTHCONDITIONS
WT-glucose-Rep1 PGCGROWTHCONDITIONS
WT-glucose-Rep2 PGCGROWTHCONDITIONS
WT-mannose PGCGROWTHCONDITIONS
WT-mucus-P1 PGCGROWTHCONDITIONS
WT-mucus-P2 PGCGROWTHCONDITIONS
1. Use Agilent software Feature Extraction to analyze spotted arrays. PGCGROWTHCONDITIONS
252978410001_B7A_CY5_BCE001MS16_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410001_B7A_CY5_BCE022DS6_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410001_B7A_CY5_BCE063MS14_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410001_B7A_CY5_ETP98015_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410002_B7A_CY5_BCE007_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410002_B7A_CY5_BCE041_MS11_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410002_B7A_CY5_BCE063_DS4_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410002_B7A_CY5_ETP98028_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410003_B7A_CY5_C35662_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410003_B7A_CY5_ETP05_007_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410003_B7A_CY5_ETP05_017_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410003_B7A_CY5_ETP98062_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410004_B7A_CY5_BCE003_DS5_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410004_B7A_CY5_BCE058_MS13_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410004_B7A_CY5_BCE069_MS9_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410004_B7A_CY5_BCE129_DS2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410005_B7A_CY5_BCE008_MS13_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410005_B7A_CY5_BCE013_DS1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410005_B7A_CY5_BCE035_MS8_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410005_B7A_CY5_BCE039_DS2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410006_B7A_CY5_ETP05_012_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410006_B7A_CY5_ETP05_019_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410006_B7A_CY5_ETP05_026_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410006_B7A_CY5_ETP05_044_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410007_B7A_CY5_BCE002_MS12_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410007_B7A_CY5_BCE021_DS7_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410007_B7A_CY5_BCE049_MS9_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410007_B7A_CY5_ETP98061_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410008_B7A_CY5_180050_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410008_B7A_CY5_ETP98103_CY3.mev.refIsIB.ou PGCGROWTHCONDITIONS
252978410008_B7A_CY5_ETP98111_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410008_B7A_CY5_TW03741_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410009_B7A_CY5_E1787_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410009_B7A_CY5_E747_0_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410009_B7A_CY5_F595C_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410009_B7A_CY5_WS3572A1.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410010_B7A_CY5_229_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410010_B7A_CY5_ICDDR_B_p13_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410010_B7A_CY5_ICDDR_B_p1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410010_B7A_CY5_ICDDR_B_p4_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410011_B7A_CY5_DS26_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410011_B7A_CY5_E1777_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410011_B7A_CY5_E9034A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410011_B7A_CY5_NN_34_1_3_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410012_B7A_CY5_42_1_C1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410012_B7A_CY5_ETEC_18_2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410012_B7A_CY5_ICDDR_B_p12_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410012_B7A_CY5_LSN02_012560_A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410013_B7A_CY5_180600_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410013_B7A_CY5_ETEC_10_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410013_B7A_CY5_TW3574_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410013_B7A_CY5_TW3585_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410014_B7A_CY5_E20738A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410014_B7A_CY5_PUTI_O26_UMN_O26_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410014_B7A_CY5_sPRH450_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410015_B7A_CY5_E1392_75_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410015_B7A_CY5_ICDDR_B_p5_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410015_B7A_CY5_ICDDR_B_p8_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410015_B7A_CY5_sPRH613_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410016_B7A_CY5_D02_2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410016_B7A_CY5_E1785_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410016_B7A_CY5_ETP98068_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410016_B7A_CY5_ICDDR_B_p11_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410017_B7A_CY5_C35776_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410017_B7A_CY5_E1788_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410017_B7A_CY5_ETEC_JURUA_18_11_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410017_B7A_CY5_ICDDR_B_p9_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410018_B7A_CY5_ARG3_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410018_B7A_CY5_E1792_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410018_B7A_CY5_MG1655_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410018_B7A_CY5_sPRH21_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410019_B7A_CY5_E1786_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410019_B7A_CY5_WS0115A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410020_B7A_CY5_179550_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410020_B7A_CY5_BCE046_DS2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410020_B7A_CY5_BCE046_DS7_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410020_B7A_CY5_ETP98114_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410021_B7A_CY5_1080200_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410021_B7A_CY5_BCE008_MS1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410021_B7A_CY5_BCE054_MS24_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410021_B7A_CY5_ETP05_046_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410022_B7A_CY5_BCE062_DS2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410022_B7A_CY5_BCE069_DS2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410022_B7A_CY5_ETP98038_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410022_B7A_CY5_ETP98042_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410023_B7A_CY5_173150_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410023_B7A_CY5_174750_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410023_B7A_CY5_178850_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410023_B7A_CY5_ETP98115_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410024_B7A_CY5_BCE018_DS6_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410024_B7A_CY5_BCE019_MS16_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410024_B7A_CY5_BCE046_MS16_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410024_B7A_CY5_BCE069_MS15_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410025_B7A_CY5_BCE007_MS11_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410025_B7A_CY5_BCE039_MS13_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410025_B7A_CY5_C35959_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410025_B7A_CY5_ETP05_050_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410026_B7A_CY5_E24377A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410026_B7A_CY5_sPRH_418_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410026_B7A_CY5_WS1896A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410026_B7A_CY5_WS2068A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410027_B7A_CY5_LSN03_016011_A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410027_B7A_CY5_sPRH_414_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410027_B7A_CY5_sPRH_420_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410027_B7A_ETEC20_10_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410028_B7A_CY5_ETP98073_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410028_B7A_CY5_TW3439_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410028_B7A_CY5_TW3576_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410028_B7A_CY5_WS3080A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410029_B7A_CY5_sPRH_403_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410029_B7A_CY5_sPRH_443_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410029_B7A_CY5_sPRH_604_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410029_B7A_CY5_sPRH_606_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410030_B7A_CY5_C36255_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410030_B7A_CY5_ETP05_008_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410030_B7A_CY5_ETP98105_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410030_B7A_ETP98066_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410031_B7A_CY5_BCE054_DS4_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410031_B7A_CY5_BCE068_MS10_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410031_B7A_CY5_BCE068_MS23.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410031_B7A_CY5_ETP05_015_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410032_B7A_CY5_BCE011_DS3_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410032_B7A_CY5_BCE049_DS3_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410032_B7A_CY5_BCE062_MS24_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410032_B7A_CY5_BCE066_DS5_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410033_B7A_CY5_BCE035_DS6_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410033_B7A_CY5_C35209_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410033_B7A_CY5_ETP_98004_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410033_B7A_CY5_ETP98056_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410034_B7A_CY5_BCE005_MS23_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410034_B7A_CY5_BCE061_DS1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410034_B7A_CY5_ETP05_038_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410034_B7A_CY5_ETP98053_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410035_B7A_CY5_BCE055_DS1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410035_B7A_CY5_ETP05_016_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410035_B7A_CY5_ETP05_020_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410035_B7A_CY5_ETP05_039_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410058_B7A_CY5_178900_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410058_B7A_CY5_179100_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410058_B7A_CY5_ETP05_009_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410058_B7A_CY5_ETP05_010_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410059_B7A_CY5_532_WS6866B1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410059_B7A_CY5_ETP05_047_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410059_B7A_CY5_ETP98097_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410059_B7A_CY5_ETP98112_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410060_B7A_CY5_ARG2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410060_B7A_CY5_C35134_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410060_B7A_CY5_E1791_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410060_B7A_CY5_WS3596_A4_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410061_B7A_CY5_COCAR07_40_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410061_B7A_CY5_COSIN07_88_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410061_B7A_CY5_COSIN07_92_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410062_B7A_CY5_DS168_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410062_B7A_CY5_PE360_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410062_B7A_CY5_WS4087_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410062_B7A_CY5_WS7179_A2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410063_B7A_CY5_B7A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410063_B7A_CY5_COSIN07_14_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410063_B7A_CY5_sPRH372_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410063_B7A_CY5_TW3452_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410064_B7A_CY5_E1789_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410064_B7A_CY5_E1790_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410064_B7A_CY5_HS_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410064_B7A_CY5_sPRH609_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410065_B7A_CY5_350C1A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410065_B7A_CY5_E2528_C1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410065_B7A_CY5_E8775_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410065_B7A_CY5_M424_C1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410066_B7A_CY5_2230_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410066_B7A_CY5_ICDDR_P_2_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410066_B7A_CY5_WS1933D_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410066_B7A_CY5_WS6582_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410067_B7A_CY5_B2C_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410067_B7A_CY5_ETEC_8_11_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410067_B7A_CY5_F5656_C1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410067_B7A_CY5_WS7162_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410068_B7A_CY5_CFT073_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410068_B7A_CY5_ICDDR_B_p_10_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410068_B7A_CY5_M408C1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410068_B7A_CY5_WS3294A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410069_B7A_CY5_278485_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410069_B7A_CY5_sPRH25_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410069_B7A_CY5_sPRH421_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410069_B7A_CY5_sPRH610_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410070_B7A_CY5_ICDDR_B_p7_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410070_B7A_CY5_NR_12_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410070_B7A_CY5_sPRH20_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410070_B7A_CY5_sPRH612_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410071_B7A_CY5_292_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410071_B7A_CY5_COCAR07_043_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410071_B7A_CY5_COSIN07_61_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410071_B7A_CY5_O157_h7_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410072_B7A_CY5_COSIN07_36_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410072_B7A_CY5_ICDDR_B_p6_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410072_B7A_CY5_O63_nm_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410072_B7A_CY5_sPRH605_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410073_B7A_CY5_214_4_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410073_B7A_CY5_E7476A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410073_B7A_CY5_WS1896_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410073_B7A_CY5_WS2173A_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410075_B7A_CY5_ETP05_011_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410075_B7A_CY5_ETP05_035_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410075_B7A_CY5_O78_h11_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410075_B7A_CY5_sPRH445_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410076_B7A_CY5_178200_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410076_B7A_CY5_C35213_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410076_B7A_CY5_C35605_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410076_B7A_CY5_ETP98109_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410077_B7A_CY5_174900_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410077_B7A_CY5_C34666_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410077_B7A_CY5_ETP05_002_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410077_B7A_CY5_ETP05_003_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410078_B7A_CY5_2_1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410078_B7A_CY5_WS2741_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410078_B7A_CY5_WS4264_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
252978410078_B7A_CY5_WS5874_A1_CY3.mev.refIsIB.out PGCGROWTHCONDITIONS
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.  PGCGROWTHCONDITIONS
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value null. PGCGROWTHCONDITIONS
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY PGCGROWTHCONDITIONS
3. Calculate the value of log2 ratio (Reference PGCGROWTHCONDITIONS
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY PGCGROWTHCONDITIONS
cells were grown in LB overnight at 37 degrees celcius. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA purified from wild type bacteri PGCGROWTHCONDITIONS
Genomic DNA purified from wild type bacteria PGCGROWTHCONDITIONS
Genomic DNA was isolated by lysozyme and proteinase K treatment. PGCGROWTHCONDITIONS
Genomic DNA was isolated by lysozyme and proteinase K treatment.   PGCGROWTHCONDITIONS
mev data obtained from the feature extraction file used, no further normalization needed PGCGROWTHCONDITIONS
None PGCGROWTHCONDITIONS
Procedures to calculate the value of log2 ratio: PGCGROWTHCONDITIONS
strain: 173150 PGCGROWTHCONDITIONS
strain: 174750 PGCGROWTHCONDITIONS
strain: 174900 PGCGROWTHCONDITIONS
strain: 178200 PGCGROWTHCONDITIONS
strain: 178850 PGCGROWTHCONDITIONS
strain: 178900 PGCGROWTHCONDITIONS
strain: 179100 PGCGROWTHCONDITIONS
strain: 179550 PGCGROWTHCONDITIONS
strain: 180050 PGCGROWTHCONDITIONS
strain: 180200 PGCGROWTHCONDITIONS
strain: 180600 PGCGROWTHCONDITIONS
strain: 2-1 PGCGROWTHCONDITIONS
strain: 214-4 PGCGROWTHCONDITIONS
strain: 2230 PGCGROWTHCONDITIONS
strain: 229-1 PGCGROWTHCONDITIONS
strain: 278485-1 PGCGROWTHCONDITIONS
strain: 292-1 PGCGROWTHCONDITIONS
strain: 350C1A PGCGROWTHCONDITIONS
strain: 42-1 C1 PGCGROWTHCONDITIONS
strain: ARG-2 PGCGROWTHCONDITIONS
strain: ARG-3 PGCGROWTHCONDITIONS
strain: B2C PGCGROWTHCONDITIONS
strain: B7A PGCGROWTHCONDITIONS
strain: BCE001, MS16 PGCGROWTHCONDITIONS
strain: BCE002, MS12 PGCGROWTHCONDITIONS
strain: BCE003, DS5 PGCGROWTHCONDITIONS
strain: BCE005, MS23 PGCGROWTHCONDITIONS
strain: BCE007 PGCGROWTHCONDITIONS
strain: BCE007, MS11 PGCGROWTHCONDITIONS
strain: BCE008_MS1 PGCGROWTHCONDITIONS
strain: BCE008, MS13 PGCGROWTHCONDITIONS
strain: BCE011, DS3 PGCGROWTHCONDITIONS
strain: BCE013, DS1 PGCGROWTHCONDITIONS
strain: BCE018, DS6 PGCGROWTHCONDITIONS
strain: BCE019, MS16 PGCGROWTHCONDITIONS
strain: BCE021, DS7 PGCGROWTHCONDITIONS
strain: BCE022DS6 PGCGROWTHCONDITIONS
strain: BCE035, DS6 PGCGROWTHCONDITIONS
strain: BCE035, MS8 PGCGROWTHCONDITIONS
strain: BCE039, DS2 PGCGROWTHCONDITIONS
strain: BCE039, MS13 PGCGROWTHCONDITIONS
strain: BCE041, MS11 PGCGROWTHCONDITIONS
strain: BCE046, DS2 PGCGROWTHCONDITIONS
strain: BCE046, DS7 PGCGROWTHCONDITIONS
strain: BCE046, MS16 PGCGROWTHCONDITIONS
strain: BCE049, DS3 PGCGROWTHCONDITIONS
strain: BCE049, MS9 PGCGROWTHCONDITIONS
strain: BCE054, DS4 PGCGROWTHCONDITIONS
strain: BCE054, MS24 PGCGROWTHCONDITIONS
strain: BCE055, DS1 PGCGROWTHCONDITIONS
strain: BCE058, MS13 PGCGROWTHCONDITIONS
strain: BCE061, DS1 PGCGROWTHCONDITIONS
strain: BCE062, DS2 PGCGROWTHCONDITIONS
strain: BCE062, MS24 PGCGROWTHCONDITIONS
strain: BCE063, DS4 PGCGROWTHCONDITIONS
strain: BCE063, MS14 PGCGROWTHCONDITIONS
strain: BCE066, DS5 PGCGROWTHCONDITIONS
strain: BCE068, MS10 PGCGROWTHCONDITIONS
strain: BCE068, MS23 PGCGROWTHCONDITIONS
strain: BCE069, DS2 PGCGROWTHCONDITIONS
strain: BCE069, MS15 PGCGROWTHCONDITIONS
strain: BCE069, MS9 PGCGROWTHCONDITIONS
strain: BCE129, DS2 PGCGROWTHCONDITIONS
strain: C-34666 PGCGROWTHCONDITIONS
strain: C-35134 PGCGROWTHCONDITIONS
strain: C-35209 PGCGROWTHCONDITIONS
strain: C-35213 PGCGROWTHCONDITIONS
strain: C-35605 PGCGROWTHCONDITIONS
strain: C-35662 PGCGROWTHCONDITIONS
strain: C-35776 PGCGROWTHCONDITIONS
strain: C-35959 PGCGROWTHCONDITIONS
strain: C-36255 PGCGROWTHCONDITIONS
strain: CFT073 PGCGROWTHCONDITIONS
strain: cocar 07-043 PGCGROWTHCONDITIONS
strain: cocar 07-40 PGCGROWTHCONDITIONS
strain: cosin 07-14 PGCGROWTHCONDITIONS
strain: cosin 07-36 PGCGROWTHCONDITIONS
strain: cosin 07-61 PGCGROWTHCONDITIONS
strain: cosin 07-88 PGCGROWTHCONDITIONS
strain: cosin 07-92 PGCGROWTHCONDITIONS
strain: D02-2 PGCGROWTHCONDITIONS
strain: DS168-1 PGCGROWTHCONDITIONS
strain: DS26-1 PGCGROWTHCONDITIONS
strain: E1392 PGCGROWTHCONDITIONS
strain: E1777 PGCGROWTHCONDITIONS
strain: E1785 PGCGROWTHCONDITIONS
strain: E1786 PGCGROWTHCONDITIONS
strain: E1787 PGCGROWTHCONDITIONS
strain: E1788 PGCGROWTHCONDITIONS
strain: E1789 PGCGROWTHCONDITIONS
strain: E1790 PGCGROWTHCONDITIONS
strain: E1791 PGCGROWTHCONDITIONS
strain: E1792 PGCGROWTHCONDITIONS
strain: E20738A PGCGROWTHCONDITIONS
strain: E24377A PGCGROWTHCONDITIONS
strain: E2528C1 PGCGROWTHCONDITIONS
strain: E7473 PGCGROWTHCONDITIONS
strain: E7476A PGCGROWTHCONDITIONS
strain: E8775 PGCGROWTHCONDITIONS
strain: E9034A PGCGROWTHCONDITIONS
strain: ETEC 10 PGCGROWTHCONDITIONS
strain: ETEC 18 PGCGROWTHCONDITIONS
strain: ETEC 20 PGCGROWTHCONDITIONS
strain: ETEC 8 PGCGROWTHCONDITIONS
strain: ETEC Jurua PGCGROWTHCONDITIONS
strain: ETP05-002 PGCGROWTHCONDITIONS
strain: ETP05-003 PGCGROWTHCONDITIONS
strain: ETP05-007 PGCGROWTHCONDITIONS
strain: ETP05-008 PGCGROWTHCONDITIONS
strain: ETP05-009 PGCGROWTHCONDITIONS
strain: ETP05-010 PGCGROWTHCONDITIONS
strain: ETP05-011 PGCGROWTHCONDITIONS
strain: ETP05-012 PGCGROWTHCONDITIONS
strain: ETP05-015 PGCGROWTHCONDITIONS
strain: ETP05-016 PGCGROWTHCONDITIONS
strain: ETP05-017 PGCGROWTHCONDITIONS
strain: ETP05-019 PGCGROWTHCONDITIONS
strain: ETP05-020 PGCGROWTHCONDITIONS
strain: ETP05-026 PGCGROWTHCONDITIONS
strain: ETP05-035 PGCGROWTHCONDITIONS
strain: ETP05-038 PGCGROWTHCONDITIONS
strain: ETP05-039 PGCGROWTHCONDITIONS
strain: ETP05-044 PGCGROWTHCONDITIONS
strain: ETP05-046 PGCGROWTHCONDITIONS
strain: ETP05-047 PGCGROWTHCONDITIONS
strain: ETP05-050 PGCGROWTHCONDITIONS
strain: ETP98004 PGCGROWTHCONDITIONS
strain: ETP98015 PGCGROWTHCONDITIONS
strain: ETP98028 PGCGROWTHCONDITIONS
strain: ETP98038 PGCGROWTHCONDITIONS
strain: ETP98042 PGCGROWTHCONDITIONS
strain: ETP98053 PGCGROWTHCONDITIONS
strain: ETP98056 PGCGROWTHCONDITIONS
strain: ETP98061 PGCGROWTHCONDITIONS
strain: ETP98062 PGCGROWTHCONDITIONS
strain: ETP98066 PGCGROWTHCONDITIONS
strain: ETP98068 PGCGROWTHCONDITIONS
strain: ETP98073 PGCGROWTHCONDITIONS
strain: ETP98097 PGCGROWTHCONDITIONS
strain: ETP98103 PGCGROWTHCONDITIONS
strain: ETP98105 PGCGROWTHCONDITIONS
strain: ETP98109 PGCGROWTHCONDITIONS
strain: ETP98111 PGCGROWTHCONDITIONS
strain: ETP98112 PGCGROWTHCONDITIONS
strain: ETP98114 PGCGROWTHCONDITIONS
strain: ETP98115 PGCGROWTHCONDITIONS
strain: F5656-C1 PGCGROWTHCONDITIONS
strain: F595C PGCGROWTHCONDITIONS
strain: HS PGCGROWTHCONDITIONS
strain: ICDDR,B_p1 PGCGROWTHCONDITIONS
strain: ICDDR,B_p10 PGCGROWTHCONDITIONS
strain: ICDDR,B_p11 PGCGROWTHCONDITIONS
strain: ICDDR,B_p12 PGCGROWTHCONDITIONS
strain: ICDDR,B_p13 PGCGROWTHCONDITIONS
strain: ICDDR,B_p2 PGCGROWTHCONDITIONS
strain: ICDDR,B_p4 PGCGROWTHCONDITIONS
strain: ICDDR,B_p5 PGCGROWTHCONDITIONS
strain: ICDDR,B_p6 PGCGROWTHCONDITIONS
strain: ICDDR,B_p7 PGCGROWTHCONDITIONS
strain: ICDDR,B_p8 PGCGROWTHCONDITIONS
strain: ICDDR,B_p9 PGCGROWTHCONDITIONS
strain: LSN02-012560 PGCGROWTHCONDITIONS
strain: LSN03-016011 PGCGROWTHCONDITIONS
strain: M408C1 PGCGROWTHCONDITIONS
strain: M424C1 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
strain: NN-34-1-3 PGCGROWTHCONDITIONS
strain: NR-12 PGCGROWTHCONDITIONS
strain: O157: h7 PGCGROWTHCONDITIONS
strain: O63:nm PGCGROWTHCONDITIONS
strain: O78: h11 PGCGROWTHCONDITIONS
strain: PE360 PGCGROWTHCONDITIONS
strain: PUTI O26 UMN O26 PGCGROWTHCONDITIONS
strain: sPRH-20 PGCGROWTHCONDITIONS
strain: sPRH-21 PGCGROWTHCONDITIONS
strain: sPRH-25 PGCGROWTHCONDITIONS
strain: sPRH-372 PGCGROWTHCONDITIONS
strain: sPRH-403 PGCGROWTHCONDITIONS
strain: sPRH-414 PGCGROWTHCONDITIONS
strain: sPRH-418 PGCGROWTHCONDITIONS
strain: sPRH-420 PGCGROWTHCONDITIONS
strain: sPRH-421 PGCGROWTHCONDITIONS
strain: sPRH-443 PGCGROWTHCONDITIONS
strain: sPRH-445 PGCGROWTHCONDITIONS
strain: sPRH-450 PGCGROWTHCONDITIONS
strain: sPRH-604 PGCGROWTHCONDITIONS
strain: sPRH-605 PGCGROWTHCONDITIONS
strain: sPRH-606 PGCGROWTHCONDITIONS
strain: sPRH-609 PGCGROWTHCONDITIONS
strain: sPRH-610 PGCGROWTHCONDITIONS
strain: sPRH-612 PGCGROWTHCONDITIONS
strain: sPRH-613 PGCGROWTHCONDITIONS
strain: TW03439 PGCGROWTHCONDITIONS
strain: TW03452 PGCGROWTHCONDITIONS
strain: TW03574 PGCGROWTHCONDITIONS
strain: TW03576 PGCGROWTHCONDITIONS
strain: TW03585 PGCGROWTHCONDITIONS
strain: TW03741 PGCGROWTHCONDITIONS
strain: WS 0115A PGCGROWTHCONDITIONS
strain: WS1896A PGCGROWTHCONDITIONS
strain: WS1896 A-1 PGCGROWTHCONDITIONS
strain: WS 1933D PGCGROWTHCONDITIONS
strain: WS2068A PGCGROWTHCONDITIONS
strain: WS 2173A PGCGROWTHCONDITIONS
strain: WS2741 A-1 PGCGROWTHCONDITIONS
strain: WS3080A PGCGROWTHCONDITIONS
strain: WS 3294A PGCGROWTHCONDITIONS
strain: WS 3572 A-1 PGCGROWTHCONDITIONS
strain: WS 3596 A-4 PGCGROWTHCONDITIONS
strain: WS4087 A-1 PGCGROWTHCONDITIONS
strain: WS4264 A-1 PGCGROWTHCONDITIONS
strain: WS5874 A-1 PGCGROWTHCONDITIONS
strain: WS6582 A-1 PGCGROWTHCONDITIONS
strain: WS 6866B-1 PGCGROWTHCONDITIONS
strain: WS 7162 A-1 PGCGROWTHCONDITIONS
strain: WS7179 A-2 PGCGROWTHCONDITIONS
CFT073 in LB, after 5 hours of growth. PGCGROWTHCONDITIONS
CFT073 in LB+PACs (100 µg PGCGROWTHCONDITIONS
CFT073_LB+PACs_rep1 PGCGROWTHCONDITIONS
CFT073_LB+PACs_rep2 PGCGROWTHCONDITIONS
CFT073_LB+PACs_rep3 PGCGROWTHCONDITIONS
CFT073_LB_rep1 PGCGROWTHCONDITIONS
CFT073_LB_rep2 PGCGROWTHCONDITIONS
CFT073_LB_rep3 PGCGROWTHCONDITIONS
Cultures of E. coli CFT073 were maintained at –80ºC in Luria-Bertani broth with 15% glycerol. Cultures were streaked onto LB agar plates and incubated (37°C, 24 h).  A single colony was inoculated into 150 mL of LB broth (in a 500 mL baffled flask).  Three inoculated flasks contained LB broth alone (controls), and three inoculated flasks were supplemented with cranberry derived PAC extract (100 µg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
growth condition: LB broth alone (control) PGCGROWTHCONDITIONS
growth condition: LB broth supplemented with cranberry PACs (100 µg PGCGROWTHCONDITIONS
One volume of bacterial culture was added to two volumes of RNAprotect Bacteria Reagent (Qiagen) and RNA was extracted using RNeasy mini kit (Qiagen).  All samples were on-column treated with DNase I. PGCGROWTHCONDITIONS
RNA extraction was performed according to the manufacturer's (Qiagen) instructions. PGCGROWTHCONDITIONS
strain: CFT073 PGCGROWTHCONDITIONS
The data were analyzed with FlexArray 1.4.1 software program (http: PGCGROWTHCONDITIONS
Comparison cya mutant with wt under glucose-limited conditions (replicate 1) PGCGROWTHCONDITIONS
Comparison cya mutant with wt under glucose-limited conditions (replicate 2) PGCGROWTHCONDITIONS
Comparison cya mutant with wt under glucose-limited conditions (replicate 3) PGCGROWTHCONDITIONS
Comparison rpoS mutant with wt under glucose-limited conditions (replicate 1) PGCGROWTHCONDITIONS
Comparison rpoS mutant with wt under glucose-limited conditions (replicate 2) PGCGROWTHCONDITIONS
Comparison rpoS mutant with wt under glucose-limited conditions (replicate 3) PGCGROWTHCONDITIONS
condition: glucose limited PGCGROWTHCONDITIONS
control PGCGROWTHCONDITIONS
cya mutant PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotype: cya mutant PGCGROWTHCONDITIONS
genotype: rpoS mutant PGCGROWTHCONDITIONS
genotype: wild-type PGCGROWTHCONDITIONS
rpoS mutant PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The data provided are the original data generated with the Jaguar software from the microarray images. The VALUEs reported represent normalized log10 (Cy5 PGCGROWTHCONDITIONS
Total RNA was isolated as described (Sambrook et al., 1989). The extracted RNA was checked for purity by gel electrophoresis and was quantified by measuring extinction spectrophotometrically at 260 nm. PGCGROWTHCONDITIONS
200µl of prepared E.coli O157 cells within LB broth is spreaded to LB agar plate, and sterilized 6mm filtered paper disk was placed on the plate tightly, where E.coli O157 is spreaded. Each filtered fractions are injected to each paper disk and Distilled water and Ampicillin were used as negative- and positive control each and then cultured at 37℃ for 24 hours. Finally the diameter of the cleared zone arisen around the paper disk was measured. PGCGROWTHCONDITIONS
50µl of total RNA of the cells affected by the Chrysanthemum herba methyl chloride fraction was isolated. The RNA extraction procedure was carried out using the RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions. Briefly, 1ml of bacterial culture was added to 2ml of RNA protect bacteria reagent (Qiagen, Inc.). Centrifugation (5000 g for 10 minutes) of the mixture was performed to precipitate the cells. The harvested cells were incubated in TE buffer with 1 mg PGCGROWTHCONDITIONS
Data analysis was carried out using the Agilent GeneSpring GX. Robust Multi-array Average (RMA) normalization performed using of signal intensity spot data which obtained by scanning process and it is indicated as a scatter plot data. Distribution of all genes which obtained result of the experiment is indicated as a histogram. Accuracy of the results of the experiment was determined through comparison of the histogram with the scatter plot data. PGCGROWTHCONDITIONS
EDL932 exposure to CL MC fraction PGCGROWTHCONDITIONS
EDL932 unexposed PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
O157_CL MC fraction vs control PGCGROWTHCONDITIONS
strain: E.coli O157:H7 EDL 932 PGCGROWTHCONDITIONS
The bacterial cells were grown at 37℃ for 17 hours on Luria-Bertani (LB) agar plate. An isolated colony was picked and inoculated into 100ml of sterilized LB broth (10g of tryptone, 5g of yeast extract and 10g of sodium chloride per liter) and incubated overnight for 17 hours at 37℃ with shaking at 250 rpm. A 1:100 dilution of the culture was performed using pre-warmed LB broth. The diluted culture was incubated at 37℃ with shaking at 250rpm until a final optical density (OD600) of 0.8 (early logarithmic phase) was attained. A further 1:10 dilution was performed using LB broth and incubated at 37℃ with shaking at 250 rpm. PGCGROWTHCONDITIONS
antibody: 9E10 Myc tag antibody PGCGROWTHCONDITIONS
antibody manufacturer: Upstate PGCGROWTHCONDITIONS
antibody: normal mouse IgG PGCGROWTHCONDITIONS
ArgR_Arginine_1 PGCGROWTHCONDITIONS
ArgR_Arginine_2 PGCGROWTHCONDITIONS
ArgR_NH4Cl_1 PGCGROWTHCONDITIONS
ArgR_NH4Cl_2 PGCGROWTHCONDITIONS
Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of ArgR-8myc and DNA was immunoprecipitated by 9E10 myc antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of ArgR-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by 9E10 myc antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of TrpR-8myc and DNA was immunoprecipitated by 9E10 myc antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of TrpR-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control. PGCGROWTHCONDITIONS
E. Coli ArgR ChIP DNA Arginine 1 PGCGROWTHCONDITIONS
E. Coli ArgR ChIP DNA Arginine 2 PGCGROWTHCONDITIONS
E. Coli ArgR ChIP DNA NH4Cl 1 PGCGROWTHCONDITIONS
E. Coli ArgR ChIP DNA NH4Cl 2 PGCGROWTHCONDITIONS
E. Coli Lrp ChIP DNA Leucine 1 PGCGROWTHCONDITIONS
E. Coli Lrp ChIP DNA Leucine 2 PGCGROWTHCONDITIONS
E. Coli Lrp ChIP DNA Leucine 3 PGCGROWTHCONDITIONS
E. Coli Lrp ChIP DNA NH4Cl 1 PGCGROWTHCONDITIONS
E. Coli Lrp ChIP DNA NH4Cl 2 PGCGROWTHCONDITIONS
E. Coli Lrp ChIP DNA NH4Cl 3 PGCGROWTHCONDITIONS
E. coli strains harboring ArgR-8myc were grown in glucose (2 g PGCGROWTHCONDITIONS
E. coli strains harboring Lrp-8myc were grown in glucose (2 g PGCGROWTHCONDITIONS
E. coli strains harboring TrpR-8myc were grown in glucose (2 g PGCGROWTHCONDITIONS
E. Coli TrpR ChIP DNA glucose PGCGROWTHCONDITIONS
E. Coli TrpR ChIP DNA Tryptophan PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype: ArgR-8myc PGCGROWTHCONDITIONS
genotype: Lrp-8myc PGCGROWTHCONDITIONS
genotype: TrpR-8myc PGCGROWTHCONDITIONS
Lrp_Leu_1 PGCGROWTHCONDITIONS
Lrp_Leu_2 PGCGROWTHCONDITIONS
Lrp_Leu_3 PGCGROWTHCONDITIONS
Lrp_NH4Cl_1 PGCGROWTHCONDITIONS
Lrp_NH4Cl_2 PGCGROWTHCONDITIONS
Lrp_NH4Cl_3 PGCGROWTHCONDITIONS
The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP PGCGROWTHCONDITIONS
treatment: glucose (2 g PGCGROWTHCONDITIONS
TrpR_glucose PGCGROWTHCONDITIONS
TrpR_Trp PGCGROWTHCONDITIONS
agent: H2O PGCGROWTHCONDITIONS
agent: ZnSO4 PGCGROWTHCONDITIONS
E. coli 0 mins PGCGROWTHCONDITIONS
E. coli 10 mins PGCGROWTHCONDITIONS
E. coli 2.5 mins PGCGROWTHCONDITIONS
E. coli 30 mins PGCGROWTHCONDITIONS
E. coli 7 mins PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5). PGCGROWTHCONDITIONS
time: 0 mins PGCGROWTHCONDITIONS
time: 10 mins PGCGROWTHCONDITIONS
time: 2.5 mins PGCGROWTHCONDITIONS
time: 30 mins PGCGROWTHCONDITIONS
time: 7 mins PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (0A1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 0A2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 0B1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 0B2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10A1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10A2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10A3) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10B1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 10B2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5A1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5A2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5B1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 2.5B2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30A1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30A2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30B1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 30B2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7A1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7A2) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7B1) PGCGROWTHCONDITIONS
Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit (slide 7B2) PGCGROWTHCONDITIONS
Zn-depleted custom-built chemostats were grown for 50 h.  At this point, ZnSO4.7H2O in water was added to a final concentration of 0.2 M in the chemostat.  A 10 ml sample of culture was taken using a polypropylene pipette tip immediately prior to Zn addition and 2.5, 7, 10 and 30 min after addition.  The culture was pipetted directly into RNAprotect (Qiagen) to stabilize RNA.  Total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.  RNA was quantified using a BioPhotometer (Eppendorf).  A control experiment was carried out in which water was added.   PGCGROWTHCONDITIONS
Butanol_Challenge_Step_1-1 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_1-2 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_2-1 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_2-2 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_3-1 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_3-2 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_4-1 PGCGROWTHCONDITIONS
Butanol_Challenge_Step_4-2 PGCGROWTHCONDITIONS
cell type: bacterial liquid culture PGCGROWTHCONDITIONS
Control_Step_1-1 PGCGROWTHCONDITIONS
Control_Step_1-2 PGCGROWTHCONDITIONS
Control_Step_2-1 PGCGROWTHCONDITIONS
Control_Step_2-2 PGCGROWTHCONDITIONS
Control_Step_3-1 PGCGROWTHCONDITIONS
Control_Step_3-2 PGCGROWTHCONDITIONS
Control_Step_4-1 PGCGROWTHCONDITIONS
Control_Step_4-2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
extracted molecule: plasmid DNA PGCGROWTHCONDITIONS
Genomic Library of E. coli was enriched via serial transfers. The cells were grown in M9 minimal media (5 g PGCGROWTHCONDITIONS
Non-challenged Library PGCGROWTHCONDITIONS
other extracted using alkalyne lysis preparation. Plasmid DNA was clean and concentrated using Zymo Clean & Concentrated -5 kit PGCGROWTHCONDITIONS
The image analysis performed using GenePix Pro 6.0 Software (Molecular Devices), normalized with MIDAS (LOWESS method), with clustering analysis in MeV (CAST) PGCGROWTHCONDITIONS
Bacterial RNA was stabilized in vivo, by using RNA protect Bacteria Reagent (Qiagen). Total RNA was isolated by using RNeasy Kits for RNA purification (Qiagen) as per the manufacturer’s protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD of 0.4 and then 0.5 mM IPTG was added to induce the protein expression PGCGROWTHCONDITIONS
Data extraction from Images was done using Feature Extraction software v 9.5.1 of Agilent. Feature extracted raw data was analyzed using GeneSpring GX V 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples. Significant genes up and down regulated showing one fold and above among the samples was identified. PGCGROWTHCONDITIONS
E. coli BL21(DE3) cells expressing catalytically inactive mutant of  M.HpyAVIB PGCGROWTHCONDITIONS
E. coli BL21(DE3) cells expressing wild-type M.HpyAVIB PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
mutant PGCGROWTHCONDITIONS
wild type PGCGROWTHCONDITIONS
antibody: normal mouse IgG (Upstate) PGCGROWTHCONDITIONS
Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug PGCGROWTHCONDITIONS
chip antibody: 9E10 Myc tag antibody PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of PurR-8myc and DNA was immunoprecipitated by 9E10 myc antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of PurR-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control. PGCGROWTHCONDITIONS
E. Coli PurR ChIP DNA Adenine 1 PGCGROWTHCONDITIONS
E. Coli PurR ChIP DNA Adenine 2 PGCGROWTHCONDITIONS
E. Coli PurR ChIP DNA glucose 1 PGCGROWTHCONDITIONS
E. Coli PurR ChIP DNA glucose 2 PGCGROWTHCONDITIONS
E. Coli PurR Input DNA Adenine 1 PGCGROWTHCONDITIONS
E. Coli PurR Input DNA Adenine 2 PGCGROWTHCONDITIONS
E. Coli PurR Input DNA glucose 1 PGCGROWTHCONDITIONS
E. Coli PurR Input DNA glucose 2 PGCGROWTHCONDITIONS
E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype: PurR-8myc PGCGROWTHCONDITIONS
growth condition: Adenine PGCGROWTHCONDITIONS
growth condition: glucose PGCGROWTHCONDITIONS
PurR_Adenine_1 PGCGROWTHCONDITIONS
PurR_Adenine_2 PGCGROWTHCONDITIONS
PurR_glucose_1 PGCGROWTHCONDITIONS
PurR_glucose_2 PGCGROWTHCONDITIONS
The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP PGCGROWTHCONDITIONS
10_HF_HP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
12_HF_LP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
13_HF_LP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
14_HF_LP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
15_HF_LP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
17_HF_HP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
18_HF_HP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
19_HF_HP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
1_HF_LP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
20_HF_HP_noDP [COPRO-Seq] PGCGROWTHCONDITIONS
2_HF_LP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
3_HF_LP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
5_HF_LP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
6_HF_HP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
7_HF_HP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
9_HF_HP_noDP_noRh [COPRO-Seq] PGCGROWTHCONDITIONS
After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were discarded. PGCGROWTHCONDITIONS
Bacteroides caccae ATCC 43185 PGCGROWTHCONDITIONS
Bacteroides ovatus ATCC 8483 PGCGROWTHCONDITIONS
Bacteroides thetaiotaomicron VPI-5482 PGCGROWTHCONDITIONS
Blautia hydrogenotrophica DSM 10507 PGCGROWTHCONDITIONS
[Clostridium] symbiosum PGCGROWTHCONDITIONS
Collinsella aerofaciens ATCC 25986 PGCGROWTHCONDITIONS
D2_14_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_14_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_1_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_2_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_4_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D2_7_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_10_m1 PGCGROWTHCONDITIONS
D3_10_m10 PGCGROWTHCONDITIONS
D3_10_m11 PGCGROWTHCONDITIONS
D3_10_m12 PGCGROWTHCONDITIONS
D3_10_m13 PGCGROWTHCONDITIONS
D3_10_m2 PGCGROWTHCONDITIONS
D3_10_m3 PGCGROWTHCONDITIONS
D3_10_m4 PGCGROWTHCONDITIONS
D3_10_m5 PGCGROWTHCONDITIONS
D3_10_m6 PGCGROWTHCONDITIONS
D3_10_m7 PGCGROWTHCONDITIONS
D3_10_m8 PGCGROWTHCONDITIONS
D3_10_m9 PGCGROWTHCONDITIONS
D3_14_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_14_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_2_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_4_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D3_7_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_10_m1 PGCGROWTHCONDITIONS
D4_10_m10 PGCGROWTHCONDITIONS
D4_10_m11 PGCGROWTHCONDITIONS
D4_10_m12 PGCGROWTHCONDITIONS
D4_10_m13 PGCGROWTHCONDITIONS
D4_10_m2 PGCGROWTHCONDITIONS
D4_10_m3 PGCGROWTHCONDITIONS
D4_10_m4 PGCGROWTHCONDITIONS
D4_10_m5 PGCGROWTHCONDITIONS
D4_10_m6 PGCGROWTHCONDITIONS
D4_10_m7 PGCGROWTHCONDITIONS
D4_10_m8 PGCGROWTHCONDITIONS
D4_10_m9 PGCGROWTHCONDITIONS
D4_14_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_14_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_1_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m11 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_2_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m10 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m12 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m13 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_4_m9 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
D4_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
Desulfovibrio piger GOR1 PGCGROWTHCONDITIONS
diet: Mouse was fed a meal of human pureed food in the following concentrations (g PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09049 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09050 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09051 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09052 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09053 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09054 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09055 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09055. PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09056 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09057 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09057. PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09058 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09059 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09620 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09621 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09622 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09623 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09624 PGCGROWTHCONDITIONS
diet: Mouse was fed Harlan Teklad Diet TD.09625 PGCGROWTHCONDITIONS
Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand. PGCGROWTHCONDITIONS
Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand.isoamyl alcohol (25:24:1, pH 8.0; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate and resuspended in 100 ul TE. The resuspension was further purified with a Qiagen PCR column and eluted into 30 ul of EB buffer. PGCGROWTHCONDITIONS
E11_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m1 PGCGROWTHCONDITIONS
E1_14_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m2 PGCGROWTHCONDITIONS
E1_14_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m3 PGCGROWTHCONDITIONS
E1_14_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m4 PGCGROWTHCONDITIONS
E1_14_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_14_m8 PGCGROWTHCONDITIONS
E1_14_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_6_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_6_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_6_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_6_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E11_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_2_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_6_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_6_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_6_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E13_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_6_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_6_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_6_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_6_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_6_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_6_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E15_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_6_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E17_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E1_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_6_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E19_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m1 PGCGROWTHCONDITIONS
E2_14_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m3 PGCGROWTHCONDITIONS
E2_14_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m4 PGCGROWTHCONDITIONS
E2_14_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m6 PGCGROWTHCONDITIONS
E2_14_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_14_m8 PGCGROWTHCONDITIONS
E2_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_2_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E2_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_14_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_2_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E3_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_1_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m1 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_4_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_6_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_6_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_6_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_6_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_6_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m2 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m3 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m4 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m5 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m6 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m7 [COPRO-Seq] PGCGROWTHCONDITIONS
E9_7_m8 [COPRO-Seq] PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
[Eubacterium] rectale ATCC 33656 PGCGROWTHCONDITIONS
Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were suspended in a solution containing 500 ul of acid-washed glass beads (Sigma-Aldrich), 500 ul of extraction buffer A (200 mM Tris [pH 8], 200 mM NaCl, 20 mM EDTA), 200 ul of 20% SDS, and 500 ul of a mixture of phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate and resuspended in 100 ul TE. The resuspension was further purified with a Qiagen PCR column and eluted into 30 ul of EB buffer. PGCGROWTHCONDITIONS
Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were treated with RNAProtect (Qiagen) and suspended in a solution containing 500 μl of acid-washed glass beads (Sigma-Aldrich), 500 μl of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 μl of 20% SDS, and 500 μl of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000 × g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5). PGCGROWTHCONDITIONS
Fecal samples obtained from mice were span frozen in liquid nitrogen and stored at -80°C and maintained at this temperature prior to processing. PGCGROWTHCONDITIONS
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA was sonicated in a biorupter sonicator, cleaned up PGCGROWTHCONDITIONS
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, gDNA was sonicated in a biorupter sonicator, cleaned up PGCGROWTHCONDITIONS
Marvinbryantia formatexigens DSM 14469 PGCGROWTHCONDITIONS
mouse feces PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion: Genomic DNA was removed with TURBO DNAse (Ambion), and then total RNA was run over two MEGAClear columns (Ambion) to deplete tRNAs and 5S rRNA. In between the two column purifications, a second DNAse digestion was performed (Baseline-ZERO Epicenter).  16S and 23S rRNA were depleted using MICROBExpress (Ambion) and custom depletion oligos (Rey et.al. 2010; JBC). PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09052 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625 PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 8-gut bacteria PGCGROWTHCONDITIONS
sample source: Fecal pellet from a mouse (c57Bl6) colonized with 9-gut bacteria PGCGROWTHCONDITIONS
time: Sample was taken after mouse was on the diet for 14 days. PGCGROWTHCONDITIONS
time: Sample was taken after mouse was on the diet for 1 days. PGCGROWTHCONDITIONS
time: Sample was taken after mouse was on the diet for 2 days. PGCGROWTHCONDITIONS
time: Sample was taken after mouse was on the diet for 4 days. PGCGROWTHCONDITIONS
time: Sample was taken after mouse was on the diet for 6 days. PGCGROWTHCONDITIONS
time: Sample was taken after mouse was on the diet for 7 days. PGCGROWTHCONDITIONS
AW1.7, steady-state continuous cultured experimental samples at 37°C PGCGROWTHCONDITIONS
AW1.7, steady-state continuous cultured experimental samples at 37°C and then 15 minutes heatshock at 50 °C PGCGROWTHCONDITIONS
Cultures were inoculated from a single colony, incubated overnight, sub-cultured with a 1% inoculum, and grown to the late exponential growth phase, corresponding to an OD600 nm of 0.6 – 0.7. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First biological repeat 37°C PGCGROWTHCONDITIONS
First biological repeat 50°C PGCGROWTHCONDITIONS
For RNA isolation, 0.5 mL of the cultures were mixed with 1 mL RNA protect (Qiagen, Ontario, Canada) and RNA was isolated using the RNeasy Mini kit (Qiagen). RNA was quantified with a Nanodrop Spectrophotometer (Thermo scientific, Wilmington, USA) and RNA quality was determined with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA samples (approximately 30 µg) were treated with 1U RNase free DNase I (Ambion, Ontario, Canada) at 37°C for 30 min and 1U RNase inhibitor (Ambion) was added prior to storage at 4°C. RNA was reverse-transcribed using the Array 900MPX Expression Array Detection Kit (Genisphere, Hatfield, USA) according to the instructions of the manufacturer. The cDNA was purified using the MinElute PCR Purification Kit (Quiagen), and the purified DNA was used for microarray and qPCR experiments. PGCGROWTHCONDITIONS
GGG10, steady-state continuous cultured experimental samples at 37°C PGCGROWTHCONDITIONS
GGG10, steady-state continuous cultured experimental samples at 37°C and then 15 minutes heatshock at 50 °C PGCGROWTHCONDITIONS
heat sensitivity: resistant PGCGROWTHCONDITIONS
heat sensitivity: sensitive PGCGROWTHCONDITIONS
Raw data were normalized and log2 transformed with the Acuity 4.0 software package, and data with low fluorescence intensities were eliminated. Genes were considered to be differentially expressed if the absolute values of log2 mean expression ratios were ≥ 1. PGCGROWTHCONDITIONS
RNA was isolated from late exponential cultures, or from late exponential cells heat-shocked by exposure to 50°C for 15 min. PGCGROWTHCONDITIONS
Second biological repeat 37°C PGCGROWTHCONDITIONS
Second biological repeat 50°C PGCGROWTHCONDITIONS
strain: AW1.7 PGCGROWTHCONDITIONS
strain: GGG10 PGCGROWTHCONDITIONS
The data did not undergo normalization across samples. PGCGROWTHCONDITIONS
Third biological repeat 37°C PGCGROWTHCONDITIONS
Third biological repeat 50°C PGCGROWTHCONDITIONS
treatment: 37°C PGCGROWTHCONDITIONS
treatment: 50°C heatshock PGCGROWTHCONDITIONS
agent: 0.05 mg PGCGROWTHCONDITIONS
agent: control PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC at 7 hrs incubation PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC at 7 hrs incubation with phloretin PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 was inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 100 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC PGCGROWTHCONDITIONS
rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.05 mg PGCGROWTHCONDITIONS
agent: 0.5% honey PGCGROWTHCONDITIONS
agent: control PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with honey PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 was inoculated in 250 ml of LB in 1000 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken with 10 g of glass wool at 100 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC PGCGROWTHCONDITIONS
rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.5% honey PGCGROWTHCONDITIONS
Cells were transferred to the fresh minimal media, mM63, in the presence or absence of histidine. The initial cell concentrations were controlled as 104-105 cells PGCGROWTHCONDITIONS
Control strain exponentially grown in the absence of histidine PGCGROWTHCONDITIONS
Control strain exponentially grown in the presence of histidine (1 mM) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: DH1 ΔhisC::cat ΔintC::Ptrc-rfp-tetR-zeocinr ΔgalK::PtetA-gfp-hisC-kanr PGCGROWTHCONDITIONS
genotype: DH1 ΔhisC::cat ΔintC::Ptrc-rfp-tetR-zeocinr ΔgalK::PtetA-gfp-kanr PGCGROWTHCONDITIONS
HisC rewired strain exponentially grown in the absence of histidine PGCGROWTHCONDITIONS
HisC rewired strain exponentially grown in the presence of histidine (1 mM) PGCGROWTHCONDITIONS
log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record. PGCGROWTHCONDITIONS
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al (2008) An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 24: 1278-1285.) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). PGCGROWTHCONDITIONS
OSU11, nurishment, biological rep 1 PGCGROWTHCONDITIONS
OSU11, nurishment, biological rep 2 PGCGROWTHCONDITIONS
OSU11, nurishment, biological rep 3 PGCGROWTHCONDITIONS
OSU11, starved, biological rep 1 PGCGROWTHCONDITIONS
OSU11, starved, biological rep 2 PGCGROWTHCONDITIONS
OSU11, starved, biological rep 3 PGCGROWTHCONDITIONS
OSU12-hisC, nurishment, biological rep 1 PGCGROWTHCONDITIONS
OSU12-hisC, nurishment, biological rep 2 PGCGROWTHCONDITIONS
OSU12-hisC, nurishment, biological rep 3 PGCGROWTHCONDITIONS
OSU12-hisC, starved, biological rep 1 PGCGROWTHCONDITIONS
OSU12-hisC, starved, biological rep 2 PGCGROWTHCONDITIONS
OSU12-hisC, starved, biological rep 3 PGCGROWTHCONDITIONS
platform_id design: EcFS_1 PGCGROWTHCONDITIONS
platform_id design: EcFS_2 PGCGROWTHCONDITIONS
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions. PGCGROWTHCONDITIONS
10 ml of cell culture was mixed with 5 ml ice cold killing buffer (20mM Tris and 5mM MgCl2 and 20mM NaN3) and cells collected by centrifugation (8000g, 4C, 3min). The supernatant was discarded and the pellet resuspended in 300μL TE with 40 μl 10% SDS and 3 μl 0.5 M EDTA. After incubation for 5 min at 65°C 750μl isopropanole was added before centrifugation at 15600 rcf for 5 min. The pellet was resuspended in 500μL TE and 2μL RNase A (25mg PGCGROWTHCONDITIONS
500 ng chrom. DNA was digested with 10U of MseI (NEB) in 10μL volume for 3h at 37°C and heat inactivated for 20 min at 65°C. To prepare adapters 100pmol of MseIlong (AGTGGGATTCCGCATGCTAGT) and MseIshortnewNo (TAACTAGCATGC)  were annealed in 8µl ddH2O by heating to 95°C for 3 min and than cooling to 70°C and subsequently to 15°C with 1°C per min. At 15°C 10µl MseI digested DNA, 2µl ligase buffer and 400U T4-ligase (NEB) were added and ligated over night. Ligase was inactivated at 65°C for 10 min. One halve of the ligation mix was digested with 20 U DpnI for 2h at 37°C in a volume of 50µl and the other halve treated similar with water instead of DpnI as control. 5µl of the DNA was amplified in a 50 µl PCR reaction with 0.2mM dNTPs, 0.5µM primer MseIlong, 10µl Phusion HF buffer and 1U Phusion DNA polymerase (Finnzymes) with the program 30sec 98°C, 20x(30sec 98°C, 30 sec 62°C, 60sec 72°C), 10 min 72°C. DNA was purified with a Qiagen PCR cleanup kit. PGCGROWTHCONDITIONS
Cell cultures were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected from 15 ml by centrifugation and washed twice with cold TBS (pH7.5).The pellet wa resuspended in 300μL TE with 40 μl 10% SDS and 3 μl 0.5 M EDTA. After incubation for 5 min at 65°C 750μl isopropanole was added before centrifugation at 15600 rcf for 5 min. The pellet was resuspended in 500μL TE and 3μL RNase A (25mg PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 0min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 15min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 16min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 17min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 35min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 50min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 30 °C to an OD450 of about 0.07 in AB glucose CAA medium, shifted to 39 °C for 70min and back to 30°C for 5min before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 37 °C to an OD450 of about 0.15 in 100 ml AB acetate medium before crosslinking. PGCGROWTHCONDITIONS
Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking. PGCGROWTHCONDITIONS
chip antibody: SeqA PGCGROWTHCONDITIONS
Cultures of E. coli MG1655 and its derivates were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected by centrifugation and washed twice with cold TBS (pH7.5). After resuspension in 1 ml lysis buffer (10mM Tris (pH 8.0), 20% sucrose, 50mM NaCl, 10mM EDTA, 10 mg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype: dnaC2 PGCGROWTHCONDITIONS
genotype: dnaC2, pMQ430 PGCGROWTHCONDITIONS
genotype: GATC-cluster::hisA PGCGROWTHCONDITIONS
genotype: GATC-cluster::srlA PGCGROWTHCONDITIONS
genotype: GATC-cluster::ter PGCGROWTHCONDITIONS
genotype: GATC-cluster::tnaA PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
input DNA PGCGROWTHCONDITIONS
Methylation in 0 min dnaC2 rep1 PGCGROWTHCONDITIONS
Methylation in 0 min dnaC2 rep2 PGCGROWTHCONDITIONS
Methylation in 15 min dnaC2 rep1 PGCGROWTHCONDITIONS
Methylation in 15 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA ChIP DNA PGCGROWTHCONDITIONS
SeqA in 0 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 0 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in 15 min dnaC2 LB PGCGROWTHCONDITIONS
SeqA in 15 min dnaC2 LB dam++ rep1 PGCGROWTHCONDITIONS
SeqA in 15 min dnaC2 LB dam++ rep2 PGCGROWTHCONDITIONS
SeqA in 15 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 15 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in 15 min dnaC2 rep3 PGCGROWTHCONDITIONS
SeqA in 16 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 16 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in 17 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 17 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in 35 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 35 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in 50 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 50 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in 5 min dnaC2 rep1 PGCGROWTHCONDITIONS
SeqA in 5 min dnaC2 rep2 PGCGROWTHCONDITIONS
SeqA in AB acetate rep1 PGCGROWTHCONDITIONS
SeqA in AB acetate rep2 PGCGROWTHCONDITIONS
SeqA in hisA GATC cluster rep1 PGCGROWTHCONDITIONS
SeqA in hisA GATC cluster rep2 PGCGROWTHCONDITIONS
SeqA in srlA GATC cluster rep1 PGCGROWTHCONDITIONS
SeqA in srlA GATC cluster rep2 PGCGROWTHCONDITIONS
SeqA in ter GATC cluster rep1 PGCGROWTHCONDITIONS
SeqA in ter GATC cluster rep2 PGCGROWTHCONDITIONS
SeqA in tnaA GATC cluster rep1 PGCGROWTHCONDITIONS
SeqA in tnaA GATC cluster rep2 PGCGROWTHCONDITIONS
Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction and normalized to the array wide average. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis. PGCGROWTHCONDITIONS
Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
strain: MG1655dnaC2 PGCGROWTHCONDITIONS
strain: TB16 PGCGROWTHCONDITIONS
strain: TWx30 PGCGROWTHCONDITIONS
strain: TWx31 PGCGROWTHCONDITIONS
strain: TWx34 PGCGROWTHCONDITIONS
strain: TWx48 PGCGROWTHCONDITIONS
treatment: control PGCGROWTHCONDITIONS
treatment: DpnI digested DNA PGCGROWTHCONDITIONS
untreated control PGCGROWTHCONDITIONS
285c PGCGROWTHCONDITIONS
All strains were grown in M9 minimal media supplemented with 25 ug PGCGROWTHCONDITIONS
Control samples (285c PGCGROWTHCONDITIONS
Data were normalized using LOWESS (MIDAS) and analyzed for statistical significance using the Rank Product method in the MultiExperimentViewer PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: 285c rpoD mutation PGCGROWTHCONDITIONS
Sigma70 LB PGCGROWTHCONDITIONS
Sigma70 LB-1 PGCGROWTHCONDITIONS
Sigma70 LB-2 PGCGROWTHCONDITIONS
Sigma70 LB-3 PGCGROWTHCONDITIONS
Sigma70 LP PGCGROWTHCONDITIONS
Sigma70 LP-1 PGCGROWTHCONDITIONS
Sigma70 LP-2 PGCGROWTHCONDITIONS
Sigma70 LP-3 PGCGROWTHCONDITIONS
The Zymo Fungal PGCGROWTHCONDITIONS
transformation: empty vector PGCGROWTHCONDITIONS
transformation: pSigma70-LB PGCGROWTHCONDITIONS
transformation: pSigma70-LP PGCGROWTHCONDITIONS
treatment: 30 C PGCGROWTHCONDITIONS
treatment: 42 C PGCGROWTHCONDITIONS
Cells from single colonies were grown on LB agar and then inoculated into liquid LB and grown to saturation. Then 50 µl was inoculated into 5 ml of K-medium and grown to saturation again. The cultures were then inoculated into the separate media as follows: 25 μl into K-medium, 50 µl into K-medium + 0.3M NaCl, 75 µl into K-medium + 0.6M urea; the final volume was 5ml in all cases. These cultures were grown overnight. The cultures were incubated in 250 ml Erlenmeyer flasks in the three media in a water bath at 30ºC. PGCGROWTHCONDITIONS
CFT073 in K-med PGCGROWTHCONDITIONS
CFT073 in NaCl PGCGROWTHCONDITIONS
CFT073 in urea PGCGROWTHCONDITIONS
CFT073 K-med biological rep 1 PGCGROWTHCONDITIONS
CFT073 K-med biological rep 2 PGCGROWTHCONDITIONS
CFT073 K-med biological rep 3 PGCGROWTHCONDITIONS
CFT073 NaCl biological rep 1 PGCGROWTHCONDITIONS
CFT073 NaCl biological rep 2 PGCGROWTHCONDITIONS
CFT073 NaCl biological rep 3 PGCGROWTHCONDITIONS
CFT073 urea biological rep 1 PGCGROWTHCONDITIONS
CFT073 urea biological rep 2 PGCGROWTHCONDITIONS
CFT073 urea biological rep 3 PGCGROWTHCONDITIONS
Escherichia coli CFT073 PGCGROWTHCONDITIONS
GCOS was used to obtain detection calls for each microarray.  The statistical difference for mRNA expression were analyzed using CarmaWeb. Affymetrix GeneChip analysis was performed using MAS for background correction, VSN for normalization, MAS for PM correction and Medianpolish for Expression.  VSN normalized data not provided by submitter. PGCGROWTHCONDITIONS
growth condition: 25 μl into K-medium PGCGROWTHCONDITIONS
growth condition: 50 µl into K-medium + 0.3M NaCl PGCGROWTHCONDITIONS
growth condition: 75 µl into K-medium + 0.6M urea PGCGROWTHCONDITIONS
Total RNA was extracted by the hot phenol–chloroform method. PGCGROWTHCONDITIONS
When the samples had reached an OD600 of 0.4-0.5, 25 ml of each culture was added to a 2.5 ml mixture of cold 95% ethanol and 5% phenol to preserve the mRNA. The cells were cooled rapidly on ice and immediately harvested by centrifugation at 4°C, and the pellet was frozen on dry ice. PGCGROWTHCONDITIONS
1. library(maanova) PGCGROWTHCONDITIONS
2. Read data: PGCGROWTHCONDITIONS
3. Log transformation: PGCGROWTHCONDITIONS
4. Normalization by Glowess method: PGCGROWTHCONDITIONS
5. Save the plot files PGCGROWTHCONDITIONS
6. close the graph: PGCGROWTHCONDITIONS
7. output: PGCGROWTHCONDITIONS
Add 100 μl 1 mg PGCGROWTHCONDITIONS
Bacterial lysis PGCGROWTHCONDITIONS
Column purification PGCGROWTHCONDITIONS
Data = read.madata(\NormInput.txt\, designfile=\Designfile1.txt\, header=TRUE, spotflag=TRUE, metarow=1, metacol=2, row=3, col=4, geneID=5, pmt=6) PGCGROWTHCONDITIONS
Data selection PGCGROWTHCONDITIONS
E. coli K12 cells, M9, 8 h PGCGROWTHCONDITIONS
E. coli K12_WT_M9_rep1 PGCGROWTHCONDITIONS
E. coli K12_WT_M9_rep2 PGCGROWTHCONDITIONS
E. coli K12 ybjN mutant cells, M9, 8 h PGCGROWTHCONDITIONS
E. coli K12_ybjN_MUTANT_M9_rep1 PGCGROWTHCONDITIONS
E. coli K12_ybjN_MUTANT_M9_rep2 PGCGROWTHCONDITIONS
E. coli K12_ybjN_MUTANT_M9_rep3 PGCGROWTHCONDITIONS
E. coli K12 ybjN over-expression cells, M9, 8 h PGCGROWTHCONDITIONS
E. coli K12_ybjN_OVER-EXPRESSION_M9_rep1 PGCGROWTHCONDITIONS
E. coli K12_ybjN_OVER-EXPRESSION_M9_rep2 PGCGROWTHCONDITIONS
E. coli K12_ybjN_OVER-EXPRESSION_M9_rep3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
genotype: ybjN mutant PGCGROWTHCONDITIONS
genotype: ybjN over-expression PGCGROWTHCONDITIONS
go to the directory: PGCGROWTHCONDITIONS
graphics.off() PGCGROWTHCONDITIONS
Grow bacteria overnight in LB medium, reinoculate in M9 minimal medium at an initial OD600 of 0.005. After eight hours growth at 34°C in M9 medium, 2 mL of RNA Protect Reagent (Qiagen) was added to 1 ml bacterial cultures (at OD600 of about 0.5-0.8) to stabilize RNA. Centrifuge for 10 min at 4000 g. Decant the supernatant. PGCGROWTHCONDITIONS
growing condition: M9 minimal medium PGCGROWTHCONDITIONS
LogData = createData(Data, n.rep=1, log.trans=TRUE) PGCGROWTHCONDITIONS
Microarray data normalization PGCGROWTHCONDITIONS
Microarray normalization is carried out using maanova function in R program version 2.2.1. Eight arrays in one slide were globally normalized using glowess method. PGCGROWTHCONDITIONS
NormalData=transform.madata(LogData, method=c(\glowess\)) PGCGROWTHCONDITIONS
norm.temp<-cbind(NormalData$metarow, NormalData$metacol,NormalData$row, NormalData$col, NormalData$geneID, NormalData$data) PGCGROWTHCONDITIONS
postscript(file=\PlotGLOWESS.ps\) PGCGROWTHCONDITIONS
postscript(file=\PlotRawData.ps\) PGCGROWTHCONDITIONS
riplot(LogData, onScreen=FALSE) PGCGROWTHCONDITIONS
riplot(NormalData, onScreen=FALSE) PGCGROWTHCONDITIONS
Sample collection from M9 medium PGCGROWTHCONDITIONS
setwd(\C:\Documents and Settings\Wang\Desktop\Erwinia in vivo\rcsC MBMA\) PGCGROWTHCONDITIONS
Stage: logarithm phase PGCGROWTHCONDITIONS
Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. A modified t-test (p-value) was computed to measure the significance associated with each differential expression value. A gene expression value was decided to be significantly different in the mutant and over-expression strains when the p-value was less than 0.05 (except otherwise mentioned) and the expression ratio was ≥ 2.0or ≤ 0.5. Gene functions were assigned using data from EcoCyc (http: PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
Total RNA isolation was performed using the RNeasy Protect Bacteria system from Qiagen. PGCGROWTHCONDITIONS
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C. PGCGROWTHCONDITIONS
write.table(norm.temp, file=\Normal_Data.csv\, sep=\,\, row.names=FALSE, col.names=TRUE, quote=FALSE) PGCGROWTHCONDITIONS
Average Normalization using GeneChip Operating Software Version 1.4 PGCGROWTHCONDITIONS
Control Strain at specific growth rate 0.5h-1 0h PGCGROWTHCONDITIONS
Control Strain at specific growth rate 0.5h-1 10h PGCGROWTHCONDITIONS
Control Strain at specific growth rate 0.5h-1 16h PGCGROWTHCONDITIONS
Control Strain at specific growth rate 0.5h-1 20h PGCGROWTHCONDITIONS
Control Strain at specific growth rate 0.5h-1 6h PGCGROWTHCONDITIONS
Control Strain at specific growth rate 0.5h-1 8h PGCGROWTHCONDITIONS
Culture samples frozen in liquid methanol PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fed batch high cell density cultivation PGCGROWTHCONDITIONS
Indole treated at specific growth rate 0.5h-1 0h PGCGROWTHCONDITIONS
Indole treated at specific growth rate 0.5h-1 10h PGCGROWTHCONDITIONS
Indole treated at specific growth rate 0.5h-1 16h PGCGROWTHCONDITIONS
Indole treated at specific growth rate 0.5h-1 5h PGCGROWTHCONDITIONS
Indole treated at specific growth rate 0.5h-1 8h PGCGROWTHCONDITIONS
Qiagen RNA extraction kit PGCGROWTHCONDITIONS
specific growth rate: 0.5h-1 PGCGROWTHCONDITIONS
strain: W3110hns∆93-1 PGCGROWTHCONDITIONS
time post-induction: 0h PGCGROWTHCONDITIONS
time post-induction: 10h PGCGROWTHCONDITIONS
time post-induction: 16h PGCGROWTHCONDITIONS
time post-induction: 20h PGCGROWTHCONDITIONS
time post-induction: 5h PGCGROWTHCONDITIONS
time post-induction: 6h PGCGROWTHCONDITIONS
time post-induction: 8h PGCGROWTHCONDITIONS
treatment group: control PGCGROWTHCONDITIONS
treatment group: indole treated PGCGROWTHCONDITIONS
Briefly, total RNA were isolated from cell culture with Total RNA Extraction Kit (RBC Bioscience) according to manufacturer's specifications. DNA was degraded by DNAse (Promega). PGCGROWTHCONDITIONS
control PGCGROWTHCONDITIONS
double mutant (PPK1 and PPX) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
exopolyphosphatase (PPX) mutant PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http: PGCGROWTHCONDITIONS
polyphosphate kinase 1 (PPK1) mutant PGCGROWTHCONDITIONS
PPK1-PPX double mutant PGCGROWTHCONDITIONS
single mutant in exopolyphosphatase (PPX) PGCGROWTHCONDITIONS
single mutant in polyphosphate kinase 1 (PPK1) PGCGROWTHCONDITIONS
zi = (Ri – mean(R))  PGCGROWTHCONDITIONS
E. coli K-12 strain BW25113 was evolved in chemostats. The cells were grown in M9 minimal media (5 g PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
growth medium: liquid culture PGCGROWTHCONDITIONS
P2-08 PGCGROWTHCONDITIONS
P2-08_R1 PGCGROWTHCONDITIONS
P2-08_R2 PGCGROWTHCONDITIONS
P2-08_R3 PGCGROWTHCONDITIONS
P2-51 PGCGROWTHCONDITIONS
P2-51_R1 PGCGROWTHCONDITIONS
P2-51_R2 PGCGROWTHCONDITIONS
P2-51_R3 PGCGROWTHCONDITIONS
P2-58 PGCGROWTHCONDITIONS
P2-58_R1 PGCGROWTHCONDITIONS
P2-58_R2 PGCGROWTHCONDITIONS
P2-58_R3 PGCGROWTHCONDITIONS
P2-66 PGCGROWTHCONDITIONS
P2-66_R1 PGCGROWTHCONDITIONS
P2-66_R2 PGCGROWTHCONDITIONS
P2-66_R3 PGCGROWTHCONDITIONS
P2-77 PGCGROWTHCONDITIONS
P2-77_R1 PGCGROWTHCONDITIONS
P2-77_R2 PGCGROWTHCONDITIONS
P2-77_R3 PGCGROWTHCONDITIONS
PF2-04 PGCGROWTHCONDITIONS
PF2-04_R1 PGCGROWTHCONDITIONS
PF2-04_R2 PGCGROWTHCONDITIONS
PF2-04_R3 PGCGROWTHCONDITIONS
PF2-08 PGCGROWTHCONDITIONS
PF2-08_R1 PGCGROWTHCONDITIONS
PF2-08_R2 PGCGROWTHCONDITIONS
PF2-08_R3 PGCGROWTHCONDITIONS
PF2-12 PGCGROWTHCONDITIONS
PF2-12_R1 PGCGROWTHCONDITIONS
PF2-12_R2 PGCGROWTHCONDITIONS
PF2-12_R3 PGCGROWTHCONDITIONS
RNA was extracted using the RNeasy Mini Kit (QIAGEN). The SuperScript indirect cDNA labeling system (Invitrogen) was used to generate cDNA. PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
The image analysis was performed using GenePix Pro 6.0 Software (Molecular Devices). Data were normalized with MIDAS (LOWESS method), with clustering analysis in MeV (CAST). PGCGROWTHCONDITIONS
wild-type PGCGROWTHCONDITIONS
wt or mutant: P2-08 PGCGROWTHCONDITIONS
wt or mutant: P2-51 PGCGROWTHCONDITIONS
wt or mutant: P2-58 PGCGROWTHCONDITIONS
wt or mutant: P2-66 PGCGROWTHCONDITIONS
wt or mutant: P2-77 PGCGROWTHCONDITIONS
wt or mutant: PF2-04 PGCGROWTHCONDITIONS
wt or mutant: PF2-08 PGCGROWTHCONDITIONS
wt or mutant: PF2-12 PGCGROWTHCONDITIONS
wt or mutant: WT @ 0.8%But PGCGROWTHCONDITIONS
cpxA-ala-1 PGCGROWTHCONDITIONS
cpxA-ala-2 PGCGROWTHCONDITIONS
cpxA mutant in Ala media PGCGROWTHCONDITIONS
cpxA mutant in Gln media PGCGROWTHCONDITIONS
cysQ-gln-1 PGCGROWTHCONDITIONS
cysQ-gln-2 PGCGROWTHCONDITIONS
cysQ mutantin Ala media PGCGROWTHCONDITIONS
cysQ mutantin Gln media PGCGROWTHCONDITIONS
dnaJ-ala-1 PGCGROWTHCONDITIONS
dnaJ-ala-2 PGCGROWTHCONDITIONS
dnaJ-gln-1 PGCGROWTHCONDITIONS
dnaJ-gln-2 PGCGROWTHCONDITIONS
dnaJ mutant in Ala media PGCGROWTHCONDITIONS
dnaJ mutant in Gln media PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
gcvT-ala-1 PGCGROWTHCONDITIONS
gcvT-ala-2 PGCGROWTHCONDITIONS
gcvT mutant in Ala media PGCGROWTHCONDITIONS
gcvT mutant in Gln media PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
hfq-gln-1 PGCGROWTHCONDITIONS
hfq-gln-2 PGCGROWTHCONDITIONS
hfq mutant in Ala media PGCGROWTHCONDITIONS
hfq mutant in Gln media PGCGROWTHCONDITIONS
Irp mutant in Ala media PGCGROWTHCONDITIONS
Irp mutant in Gln media PGCGROWTHCONDITIONS
LB-grown overnight cultures were pelleted by centrifugation, washed, and resuspended in M9-glutamine of M9-alanine media.  Cultures were shaken at 250 rpm at 37C.  Samples were taken in mid-exponential phase (OD600 =0.15 for glutamine and OD600=0.2 for alanine on an Ultraspec 3100 pro) after ~5 generations of growth in the media. PGCGROWTHCONDITIONS
lrp-gln-1 PGCGROWTHCONDITIONS
lrp-gln-2 PGCGROWTHCONDITIONS
pgi-ala-1 PGCGROWTHCONDITIONS
pgi-ala-2 PGCGROWTHCONDITIONS
pgi mutantin Ala media PGCGROWTHCONDITIONS
pgi mutantin Gln media PGCGROWTHCONDITIONS
strain: AH28 PGCGROWTHCONDITIONS
strain: ZD1 PGCGROWTHCONDITIONS
strain: ZD26 PGCGROWTHCONDITIONS
strain: ZD51 PGCGROWTHCONDITIONS
strain: ZD56 PGCGROWTHCONDITIONS
strain: ZD59 PGCGROWTHCONDITIONS
strain: ZD60 PGCGROWTHCONDITIONS
strain: ZD8 PGCGROWTHCONDITIONS
The ‘LogRatio’ value was used in subsequent analyses.  All values for the same ORF were averaged as were the values from the two biological replicates performed for each comparison. PGCGROWTHCONDITIONS
When the cultures reached the desired density, 2 ml of culture was added to 4 ml of RNAprotect Bacteria Reagent (Qiagen).  The mixture was incubated at room temperature for 5 min and then centrifuged at 5000 g for 10 min.  The supernatant was removed and the pellets were stored at -80C.  RNA was isolated using the Norgen Total RNA Purification Kit (Product #17200) according to the manufacturer’s directions except in the last step the RNA was eluted in 35 uL. PGCGROWTHCONDITIONS
wild-type in ala media_1 PGCGROWTHCONDITIONS
wild-type in ala media_2 PGCGROWTHCONDITIONS
wild-type in gln media_1 PGCGROWTHCONDITIONS
wild-type in gln media_2 PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with DMSO PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with indole-3-acetaldehyde PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 was inoculated in 100 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken with 4 g of glass wool at 250 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
RNA extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.1 mg PGCGROWTHCONDITIONS
RNA extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with DMSO PGCGROWTHCONDITIONS
serotype: O157:H7 PGCGROWTHCONDITIONS
strain: EDL933 PGCGROWTHCONDITIONS
Cells in log phase under ethanol stress PGCGROWTHCONDITIONS
Cells were grown at 37°C in Luria-Bertani (LB) medium containing 50 μg PGCGROWTHCONDITIONS
Data were analyzed using GeneChip Operating Software Version 1.4 (Affymetrix) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: ethanol-tolerant mutant E1 of IrrE PGCGROWTHCONDITIONS
genotype: wild type IrrE PGCGROWTHCONDITIONS
mutant E1, biological rep1 PGCGROWTHCONDITIONS
mutant E1, biological rep2 PGCGROWTHCONDITIONS
mutant E1, biological rep3 PGCGROWTHCONDITIONS
strain: DH5a PGCGROWTHCONDITIONS
The cells were centrifuged when they reached the log phase, and then rapidly chilled and stored in liquid nitrogen until used for the DNA microarray assay PGCGROWTHCONDITIONS
Total RNA was isolated from the cells stored in liquid nitrogen using TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and RNeasy MinElute Cleanup Kits (Qiagen, Valencia, CA, USA) PGCGROWTHCONDITIONS
wild type E0, biological rep1 PGCGROWTHCONDITIONS
wild type E0, biological rep2 PGCGROWTHCONDITIONS
wild type E0, biological rep3 PGCGROWTHCONDITIONS
E. coli cultutures were grown in M9 media using standard protocol, to log phase (OD600 of 0.7-0.8) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: gss mutant PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
gss-1 PGCGROWTHCONDITIONS
gss-2 PGCGROWTHCONDITIONS
gss-3 PGCGROWTHCONDITIONS
MAS 5.0 PGCGROWTHCONDITIONS
No treatment, just comparison of RNAs from wild type and mutant. PGCGROWTHCONDITIONS
Trizol extraction of total RNA was performed according to the manufacturer's instructions. PGCGROWTHCONDITIONS
WT-1 PGCGROWTHCONDITIONS
WT-2 PGCGROWTHCONDITIONS
WT-3 PGCGROWTHCONDITIONS
Affymetrix GeneChip Operating Software (GCOS) Version 1.4  Details: Intra-chip normalizations were performed using Affymetrix Gene Chip Operating Software (GCOS). Default statistical parameters were used to normalize each chip to the same target intensity (1500) as described in the Affymetrix GeneChip Expression Analysis manual. All nine possible inter-chip comparisons were performed in GCOS. The data were subsequently exported to a Microsoft Excel spreadsheet for manipulation. Consensus “detection p-value”, “change p-value”, and “signal log ratios” were calculated, and the default E. coli array p-value cutoff parameters were applied to these consensus values to estimate the transcript change between two conditions and the transcript presence under each condition. Background-subtracted data sets were used to calculate up-regulated and down-regulated genes based on fold changes of greater than 2. PGCGROWTHCONDITIONS
E.coli cells  grown with aeration in LB media at 37º C until early log phase (0.4) and were treated with PGCGROWTHCONDITIONS
E. coli K12 strain JM109 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
JM109-1, biological rep1 PGCGROWTHCONDITIONS
JM109-2, biological rep2 PGCGROWTHCONDITIONS
JM109-3, biological rep3 PGCGROWTHCONDITIONS
JM109 GLY-1, biological rep1 PGCGROWTHCONDITIONS
JM109 GLY-2, biological rep2 PGCGROWTHCONDITIONS
JM109 GLY-3, biological rep3 PGCGROWTHCONDITIONS
Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA).Disrupt about 107cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4 - 25 C. Remove the supernatant and wash the RNA pellet ( by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4 - 25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3 - 5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Using an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA. PGCGROWTHCONDITIONS
treatment: 200 mM glyphosate shock for 1 h PGCGROWTHCONDITIONS
Treatment protocol- E.coli cells grown in LB media with  at 37C until early log phase (0.4), then were treated with 200 mM glyphosate for 1 h,after that the cells were harvested to extract RNA. PGCGROWTHCONDITIONS
treatment: without salt shock PGCGROWTHCONDITIONS
BW25113 mqsR PGCGROWTHCONDITIONS
cell type: Planktonic cells harvested at a turbidity of 0.5 at 600 nm, adjusted to the turbidity at 1, and then exposed to 20 μg PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
medium: LB PGCGROWTHCONDITIONS
strains: K-12 BW25113 PGCGROWTHCONDITIONS
temp: 37ºC PGCGROWTHCONDITIONS
The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. Planktonic cells were grown to a turbidity of 0.5 at 600 nm in LB medium with 1 mM IPTG at 37 °C, adjusted the turbidity to 1, and exposed to 20 μg PGCGROWTHCONDITIONS
The overnight culture (0.25 mL) was used to inoculate 25 mL of fresh LB medium. Planktonic cells were grown to a turbidity of 0.5 at 600 nm in LB medium with 1 mM IPTG at 37 °C, adjusted the turbidity to 1, and exposed to 20 μg PGCGROWTHCONDITIONS
time: 1 h with 20 μg PGCGROWTHCONDITIONS
EM1456 wild-type pNM12#1 +arabinose PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
experiment #115 PGCGROWTHCONDITIONS
experiment #116 PGCGROWTHCONDITIONS
experiment #203 PGCGROWTHCONDITIONS
experiment #204 PGCGROWTHCONDITIONS
experiment #205 PGCGROWTHCONDITIONS
experiment #206 PGCGROWTHCONDITIONS
experiment #303 PGCGROWTHCONDITIONS
experiment #305 PGCGROWTHCONDITIONS
experiment #306 PGCGROWTHCONDITIONS
fur mutant pBAD-ryhB#1 + arabinose PGCGROWTHCONDITIONS
fur mutant pBAD-ryhB#2 + arabinose PGCGROWTHCONDITIONS
fur mutant pNM12#1 + arabinose PGCGROWTHCONDITIONS
fur mutant pNM12#2 + arabinose PGCGROWTHCONDITIONS
Microarray suite 5.0 PGCGROWTHCONDITIONS
Strain EM1453 wild-type pBAD-ryhB#1 + arabinose PGCGROWTHCONDITIONS
wild-type pBAD-ryhB#1 + arabinose PGCGROWTHCONDITIONS
wild-type pBAD-ryhB#1 +FeSO4 + arabinose PGCGROWTHCONDITIONS
wild-type pBAD-ryhB #2 + arabinose PGCGROWTHCONDITIONS
wild-type pBAD-ryhB#2 +FeSO4 + arabinose PGCGROWTHCONDITIONS
wild-type pNM12#1 +arabinose PGCGROWTHCONDITIONS
wild-type pNM12#1 +FeSO4 + arabinose PGCGROWTHCONDITIONS
wild-type pNM12#2 + arabinose PGCGROWTHCONDITIONS
wild-type pNM12#2 +FeSO4 + arabinose PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
N3433 (rne deletion) pBADRNE in LB at 30 degrees C PGCGROWTHCONDITIONS
N3433 (rne deletion) pBAD-RNE w PGCGROWTHCONDITIONS
N3433 (rne deletion) pNRNE5 at 30 degrees C PGCGROWTHCONDITIONS
N3433 (rne deletion) pRNG3 at 30 degrees C PGCGROWTHCONDITIONS
N3433 (rng deletion) in LB at 30 degrees C PGCGROWTHCONDITIONS
N3433 (rng deletion) LB at 30 C PGCGROWTHCONDITIONS
N3433 (wt) in LB at 30 degrees C PGCGROWTHCONDITIONS
N3433 (wt) pPM30 in LB at 30 degrees C PGCGROWTHCONDITIONS
N3433 (wt) pRNG3 in LB at 30 degrees PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rne deletion) pBADRNE in LB at 30 degrees C Trial B * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rne deletion) pBAD-RNE w PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rne deletion) pNRNE5 at 30 degrees C Trial A * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rne deletion) pNRNE5 at 30 degrees C Trial B * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rne deletion) pRNG3 at 30 degrees C Trial A * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rne deletion) pRNG3 at 30 degrees C Trial B * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (rng deletion) in LB at 30 degrees C Trial B PGCGROWTHCONDITIONS
N3433 (wt)  vs N3433 (rng deletion) LB at 30 C Trial A * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (wt) pRNG3 in LB at 30 degrees Trial A * PGCGROWTHCONDITIONS
N3433 (wt) vs N3433 (wt) pRNG3 in LB at 30 degrees Trial B * PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
A10:LJ110 del pdhr MMAcetat PGCGROWTHCONDITIONS
A11:LJ110 pTM30 MMAcetat PGCGROWTHCONDITIONS
A12:LJ110 pTM30pdhr MMAcetat PGCGROWTHCONDITIONS
A1:LJ110 LBo PGCGROWTHCONDITIONS
A2:LJ110 del pdhr LBo PGCGROWTHCONDITIONS
A3:LJ110 pTM30 LBo PGCGROWTHCONDITIONS
A4:LJ110 pTM30pdhr LBo PGCGROWTHCONDITIONS
A5:LJ110 MMPyruvat PGCGROWTHCONDITIONS
A6:LJ110 del pdhr MMPyruvat PGCGROWTHCONDITIONS
A7:LJ110 pTM30 MMPyruvat PGCGROWTHCONDITIONS
A8:LJ110 pTM30pdhr MMPyruvat PGCGROWTHCONDITIONS
A9:LJ110 MMAcetat PGCGROWTHCONDITIONS
B10:LJ110 del pdhr MMAcetat PGCGROWTHCONDITIONS
B11:LJ110 pTM30 MMAcetat PGCGROWTHCONDITIONS
B12:LJ110 pTM30pdhr MMAcetat PGCGROWTHCONDITIONS
B1:LJ110 LBo PGCGROWTHCONDITIONS
B2:LJ110 del pdhr LBo PGCGROWTHCONDITIONS
B3:LJ110 pTM30 LBo PGCGROWTHCONDITIONS
B4:LJ110 pTM30pdhr LBo PGCGROWTHCONDITIONS
B5:LJ110 MMPyruvat PGCGROWTHCONDITIONS
B6:LJ110 del pdhr MMPyruvat PGCGROWTHCONDITIONS
B7:LJ110 pTM30 MMPyruvat PGCGROWTHCONDITIONS
B8:LJ110 pTM30pdhr MMPyruvat PGCGROWTHCONDITIONS
B9:LJ110 MMAcetat PGCGROWTHCONDITIONS
background strain: LJ110 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Expression values were calculated by the software package Feature Extraction 10.5.1.1 using protocol GE1_105_Dec08 (Agilent Technologies; Waldbronn, Germany) PGCGROWTHCONDITIONS
genetic modification: empty plasmid (LJ110 PGCGROWTHCONDITIONS
genetic modification: PdhR knockout mutant (LJ110deltapdhR) PGCGROWTHCONDITIONS
genetic modification: PdhR overexpression strain (LJ110 PGCGROWTHCONDITIONS
genetic modification: wild type LJ110 PGCGROWTHCONDITIONS
LJ110 del pdhr LBo PGCGROWTHCONDITIONS
LJ110 del pdhr MMAcetat PGCGROWTHCONDITIONS
LJ110 del pdhr MMPyruvat PGCGROWTHCONDITIONS
LJ110 LBo PGCGROWTHCONDITIONS
LJ110 MMAcetat PGCGROWTHCONDITIONS
LJ110 MMPyruvat PGCGROWTHCONDITIONS
LJ110 pTM30 LBo PGCGROWTHCONDITIONS
LJ110 pTM30 MMAcetat PGCGROWTHCONDITIONS
LJ110 pTM30 MMPyruvat PGCGROWTHCONDITIONS
LJ110 pTM30pdhr LBo PGCGROWTHCONDITIONS
LJ110 pTM30pdhr MMAcetat PGCGROWTHCONDITIONS
LJ110 pTM30pdhr MMPyruvat PGCGROWTHCONDITIONS
MMAcetat PGCGROWTHCONDITIONS
MMPyruvat PGCGROWTHCONDITIONS
RNAeasy PGCGROWTHCONDITIONS
CRE Multi 0uM Rep1 Plasmid PGCGROWTHCONDITIONS
CRE Multi 0uM Rep2 Plasmid PGCGROWTHCONDITIONS
CRE Multi 100uM Rep1 Plasmid PGCGROWTHCONDITIONS
CRE Multi 100uM Rep2 Plasmid PGCGROWTHCONDITIONS
CRE Single 100uM Rep1 Plasmid PGCGROWTHCONDITIONS
CRE Single 100uM Rep2 Plasmid PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
HEK293T PGCGROWTHCONDITIONS
IFNB Multi SeV0 Rep1 Plasmid PGCGROWTHCONDITIONS
IFNB Multi SeV10 Rep1 Plasmid PGCGROWTHCONDITIONS
IFNB Single SeV10 Rep1 Plasmid PGCGROWTHCONDITIONS
Plasmid pool PGCGROWTHCONDITIONS
reporter: CRE multi-hit PGCGROWTHCONDITIONS
reporter: CRE single-hit PGCGROWTHCONDITIONS
reporter: IFNB multi-hit PGCGROWTHCONDITIONS
reporter: IFNB single-hit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: plasmid pool PGCGROWTHCONDITIONS
To infer the tag copy numbers in each Tag-Seq library, all sequence reads were examined, regardless of their quality scores. If the first ten nucleotides of a read perfectly matched one of the 13,000 or 27,000 designed tags and the remaining nucleotides matched the expected upstream MPRA construct sequence, this was counted as one occurrence of that tag. All reads that did not meet this criterion were discarded. PGCGROWTHCONDITIONS
Total RNA was isolated from cell lysates using RNeasy kits (Qiagen). mRNA was extracted from total RNA using MicroPoly(A)Purist™ kits (Ambion) and treated with DNase I using the Turbo DNA-free™ kit (Ambion). First-strand cDNA was synthesized from 400-700 ng mRNA using High Capacity RNA-to-cDNA kits (Applied Biosystems).  Tag-Seq sequencing libraries were generated directly from 12% of a cDNA reaction or 50 ng plasmid DNA by 26 cycle PCR using Pfu Ultra HS DNA polymerase 2x master mix (Agilent) and primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG (where XXXXXXXX is a library-specific index sequence). The resultant PCR products were size-selected using 2% agarose E-Gel EX (Invitrogen). PGCGROWTHCONDITIONS
treatment: N PGCGROWTHCONDITIONS
0 min PGCGROWTHCONDITIONS
10 min PGCGROWTHCONDITIONS
30 min PGCGROWTHCONDITIONS
60 min PGCGROWTHCONDITIONS
Agilent Feature Extraction Software v. 9.5.3.1 was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Escherichia coli 0 min vs 10 min Rep1 PGCGROWTHCONDITIONS
Escherichia coli 10 min vs 0 min Rep2 PGCGROWTHCONDITIONS
Escherichia coli 30 min vs 60 min Rep1 PGCGROWTHCONDITIONS
Escherichia coli 60 min vs 30 min Rep2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
One conditions: 5% (v PGCGROWTHCONDITIONS
Overnight culture of E. coli BW25113 in LB was diluted in M9 minimal medium with supplements to OD600=0.02 and was incubated at 37 Ceilsus degree with shaking at 250rpm until its OD600 reached 0.1. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
time: 30 min PGCGROWTHCONDITIONS
time: 60 min PGCGROWTHCONDITIONS
Total RNA was extracted from 5ml cell culture at 0, 10, 30 and 60 min incubation after addition of 5% isooctane using RNeasy mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol PGCGROWTHCONDITIONS
treatment: 5 percent isooctane PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
normalized using lcDNA PGCGROWTHCONDITIONS
ppsA mutant 15 min (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 15 min (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 1 hour (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 1 hour (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 1 hour (2) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 1 hour (2) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 1 hour (3) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 1 hour (3) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 2 hour (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 2 hour (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 2 hour (2) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 2 hour (2) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 2 hour (3) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 2 hour (3) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 30 min (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 30 min (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 3 hour (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 3 hour (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 3 hour (2) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 3 hour (2) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 3 hour (3) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 3 hour (3) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 4 hour (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 4 hour (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 4 hour (2) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 4 hour (2) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 4 hour (3) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 4 hour (3) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 5 hour (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 5 hour (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 5 hour (2) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 5 hour (2) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 5 min (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 5 min (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 6 hour (1) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 6 hour (1) slide 2 PGCGROWTHCONDITIONS
ppsA mutant 6 hour (2) slide 1 PGCGROWTHCONDITIONS
ppsA mutant 6 hour (2) slide 2 PGCGROWTHCONDITIONS
reference sample harvested immediately prior to glucose to acetate shift PGCGROWTHCONDITIONS
strain BW25113 PGCGROWTHCONDITIONS
Strain BW25113 PGCGROWTHCONDITIONS
Strain BW25113  PGCGROWTHCONDITIONS
strain BW25113 ppsA deletion PGCGROWTHCONDITIONS
time course sample harvested after 15 min of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 1 hour of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 2 hour of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 30 min of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 3 hour of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 4 hour of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 5 hour of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 5 min of glucose to acetate shift PGCGROWTHCONDITIONS
time course sample harvested after 6 hour of glucose to acetate shift PGCGROWTHCONDITIONS
wild-type 15 min (1) slide 1 PGCGROWTHCONDITIONS
wild-type 15 min (1) slide 2 PGCGROWTHCONDITIONS
wild-type 15 min (2) slide 1 PGCGROWTHCONDITIONS
wild-type 15 min (2) slide 2 PGCGROWTHCONDITIONS
wild-type 1 hour (1) slide 1 PGCGROWTHCONDITIONS
wild-type 1 hour (1) slide 2 PGCGROWTHCONDITIONS
wild-type 1 hour (2) slide 2 PGCGROWTHCONDITIONS
wild-type 1 hour (3) slide 1 PGCGROWTHCONDITIONS
wild-type 1 hour (3) slide 2 PGCGROWTHCONDITIONS
wild-type 2 hour (1) slide 1 PGCGROWTHCONDITIONS
wild-type 2 hour (1) slide 2 PGCGROWTHCONDITIONS
wild-type 2 hour (2) slide 1 PGCGROWTHCONDITIONS
wild-type 2 hour (2) slide 2 PGCGROWTHCONDITIONS
wild-type 2 hour (3) slide 1 PGCGROWTHCONDITIONS
wild-type 2 hour (3) slide 2 PGCGROWTHCONDITIONS
wild-type 30 min (1) slide 1 PGCGROWTHCONDITIONS
wild-type 30 min (1) slide 2 PGCGROWTHCONDITIONS
wild-type 30 min (2) slide 1 PGCGROWTHCONDITIONS
wild-type 30 min (2) slide 2 PGCGROWTHCONDITIONS
wild-type 3 hour (1) slide 1 PGCGROWTHCONDITIONS
wild-type 3 hour (1) slide 2 PGCGROWTHCONDITIONS
wild-type 3 hour (2) slide 1 PGCGROWTHCONDITIONS
wild-type 3 hour (2) slide 2 PGCGROWTHCONDITIONS
wild-type 3 hour (3) slide 1 PGCGROWTHCONDITIONS
wild-type 3 hour (3) slide 2 PGCGROWTHCONDITIONS
wild-type 4 hour (1) slide 1 PGCGROWTHCONDITIONS
wild-type 4 hour (1) slide 2 PGCGROWTHCONDITIONS
wild-type 4 hour (2) slide 1 PGCGROWTHCONDITIONS
wild-type 4 hour (2) slide 2 PGCGROWTHCONDITIONS
wild-type 4 hour (3) slide 1 PGCGROWTHCONDITIONS
wild-type 4 hour (3) slide 2 PGCGROWTHCONDITIONS
wild-type 5 hour (1) slide 1 PGCGROWTHCONDITIONS
wild-type 5 hour (1) slide 2 PGCGROWTHCONDITIONS
wild-type 5 hour (2) slide 1 PGCGROWTHCONDITIONS
wild-type 5 hour (2) slide 2 PGCGROWTHCONDITIONS
wild-type 5min (1) slide 1 PGCGROWTHCONDITIONS
wild-type 5min (1) slide 2 PGCGROWTHCONDITIONS
wild-type 5min (2) slide 1 PGCGROWTHCONDITIONS
wild-type 5min (2) slide 2 PGCGROWTHCONDITIONS
wild-type 6 hour (1) slide 1 PGCGROWTHCONDITIONS
wild-type 6 hour (1) slide 2 PGCGROWTHCONDITIONS
wild-type 6 hour (2) slide 1 PGCGROWTHCONDITIONS
wild-type 6 hour (2) slide 2 PGCGROWTHCONDITIONS
After 6 hours of growth both control and test strains were induced with 0.5mM IPTG and harvested 2 hours post-induction. PGCGROWTHCONDITIONS
EGS084 PGCGROWTHCONDITIONS
EGS084_control_rep_1 PGCGROWTHCONDITIONS
EGS084_control_rep_2 PGCGROWTHCONDITIONS
EGS084_control_rep_3 PGCGROWTHCONDITIONS
EGS084_control_rep_4 PGCGROWTHCONDITIONS
EGS084_control_rep_5 PGCGROWTHCONDITIONS
EGS084_control_rep_6 PGCGROWTHCONDITIONS
EGS212 PGCGROWTHCONDITIONS
EGS212_MlfabH_rep_1 PGCGROWTHCONDITIONS
EGS212_MlfabH_rep_2 PGCGROWTHCONDITIONS
EGS212_MlfabH_rep_3 PGCGROWTHCONDITIONS
EGS212_MlfabH_rep_4 PGCGROWTHCONDITIONS
EGS212_MlfabH_rep_5 PGCGROWTHCONDITIONS
Escherichia coli DH1 ∆fadE control and test strains were seeded with OD600nm 0.03 overnight cultures into 15ml tryptic soy broth media and grown at 37°C with 200rpm agitation. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotype: ∆fadE with overexpression of 'tesA and MlfabH via an IPTG-inudcible promoter PGCGROWTHCONDITIONS
genotype: ∆fadE with overexpression of 'tesA via an IPTG-inudcible promoter PGCGROWTHCONDITIONS
phenotype: normal PGCGROWTHCONDITIONS
phenotype: small improvement in methyl ketone production PGCGROWTHCONDITIONS
substrain: DH1 PGCGROWTHCONDITIONS
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA concentration was determined on a Nanodrop ND-1000 (Thermo Scientific) and RNA quality was determined by analysis with an Agilent 2100 bioanalyzer. PGCGROWTHCONDITIONS
E. coli MG1655 10 min after TMP+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 10 min after TMP+adenine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 10 min after TMP+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 10 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 10 min after TMP treatment in LB media PGCGROWTHCONDITIONS
E. coli MG1655 10 min after TMP treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 120 min after TMP+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 120 min after TMP+adenine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 120 min after TMP+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 120 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 120 min after TMP treatment in LB media PGCGROWTHCONDITIONS
E. coli MG1655 120 min after TMP treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 30 min after TMP+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 30 min after TMP+adenine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 30 min after TMP+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 30 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 30 min after TMP treatment in LB media PGCGROWTHCONDITIONS
E. coli MG1655 30 min after TMP treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 60 min after TMP+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 60 min after TMP+adenine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 60 min after TMP+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 60 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 60 min after TMP treatment in LB media PGCGROWTHCONDITIONS
E. coli MG1655 60 min after TMP treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 90 min after TMP+adenine+glycine+methionine treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 90 min after TMP treatment in M9 media PGCGROWTHCONDITIONS
E. coli MG1655 mid-log phase in LB media PGCGROWTHCONDITIONS
E. coli MG1655 mid-log phase in M9 media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
LBTMP50_10min PGCGROWTHCONDITIONS
LBTMP50_120min PGCGROWTHCONDITIONS
LBTMP50_30min PGCGROWTHCONDITIONS
LBTMP50_60min PGCGROWTHCONDITIONS
M9TMP5_10min PGCGROWTHCONDITIONS
M9TMP5_120min PGCGROWTHCONDITIONS
M9TMP5_30min PGCGROWTHCONDITIONS
M9TMP5_60min PGCGROWTHCONDITIONS
M9TMP5_90min PGCGROWTHCONDITIONS
M9TMP5_AdAA_10min PGCGROWTHCONDITIONS
M9TMP5_AdAA_120min PGCGROWTHCONDITIONS
M9TMP5_AdAA_30min PGCGROWTHCONDITIONS
M9TMP5_AdAA_60min PGCGROWTHCONDITIONS
M9TMP5_AdAA_90min PGCGROWTHCONDITIONS
M9_TMP5_THY_Ad_AA_10min PGCGROWTHCONDITIONS
M9_TMP5_THY_Ad_AA_120min PGCGROWTHCONDITIONS
M9_TMP5_THY_Ad_AA_30min PGCGROWTHCONDITIONS
M9_TMP5_THY_Ad_AA_60min PGCGROWTHCONDITIONS
M9TMP_AA_10min PGCGROWTHCONDITIONS
M9TMP_AA_120min PGCGROWTHCONDITIONS
M9TMP_AA_30min PGCGROWTHCONDITIONS
M9TMP_AA_60min PGCGROWTHCONDITIONS
M9TMP_Ad_10min PGCGROWTHCONDITIONS
M9TMP_Ad_120min PGCGROWTHCONDITIONS
M9TMP_Ad_30min PGCGROWTHCONDITIONS
M9TMP_Ad_60min PGCGROWTHCONDITIONS
Overnight cultures were resuspended in fresh medium and TMP was added when the optical density (O.D. 600 nm) of the culture reached 0.3-0.4. PGCGROWTHCONDITIONS
Raw fluorescence intensity data were normalized in R (http: PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Time-point samples were taken every 15-30 minutes from 15 minutes to 2 hours post treatment. PGCGROWTHCONDITIONS
Total RNA samples were purified using the Qiagen RNeasy kit (Chatsworth, CA) according to the manufacturer’s protocol. PGCGROWTHCONDITIONS
20 ug of Total RNA from MG1655 (Repaired NCM 3416) in LB at 30 degrees OD 600=0.8 PGCGROWTHCONDITIONS
20 ug of Total RNA from MG1655 (Repaired NCM 3416) in M9 at 30 degrees OD 600=0.8 PGCGROWTHCONDITIONS
2 ug of Genomic MG 1655 (Repaired NCM 3416) DNA PGCGROWTHCONDITIONS
2 ug of MG1655 (Repaired NCM 3416) Genomic DNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Transcript Abundance in LB at 30 degrees OD600=0.8 Trial A PGCGROWTHCONDITIONS
Transcript Abundance in LB at 30 degrees OD600=0.8 Trial B PGCGROWTHCONDITIONS
Transcript Abundance in M9 at 30 degrees OD600=0.8 Trial A PGCGROWTHCONDITIONS
Transcript Abundance in M9 at 30 degrees OD600=0.8 Trial B PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
2' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C PGCGROWTHCONDITIONS
2' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A PGCGROWTHCONDITIONS
2' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B PGCGROWTHCONDITIONS
4' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C PGCGROWTHCONDITIONS
4' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A PGCGROWTHCONDITIONS
4' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B PGCGROWTHCONDITIONS
6' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C PGCGROWTHCONDITIONS
6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A PGCGROWTHCONDITIONS
6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B PGCGROWTHCONDITIONS
8' RNA Decay of MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose Trial A PGCGROWTHCONDITIONS
8' RNA Decay of MG1655 (Repaired NCM 3416) in LB at 30 C PGCGROWTHCONDITIONS
8' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MG1655 2' post rif PGCGROWTHCONDITIONS
MG1655 4' post rif PGCGROWTHCONDITIONS
MG1655 6' post rif PGCGROWTHCONDITIONS
MG1655 8' post rif PGCGROWTHCONDITIONS
MG1655 at 30 Degrees PGCGROWTHCONDITIONS
MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose PGCGROWTHCONDITIONS
MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose 8' post rif PGCGROWTHCONDITIONS
MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose PGCGROWTHCONDITIONS
MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 2' post rif PGCGROWTHCONDITIONS
MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 4' post rif PGCGROWTHCONDITIONS
MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 6' post rif PGCGROWTHCONDITIONS
MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose 8' post rif PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
lrp- + Leu vs. lrp-  - Leu PGCGROWTHCONDITIONS
lrp- - Leu vs. wt - Leu PGCGROWTHCONDITIONS
lrp- + Leu vs. wt - Leu PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
\W3110 lrp- at OD420~0.3 in MOPS  (ile, val, thi), 20 ug total, 10 ug pdN6 \ PGCGROWTHCONDITIONS
\W3110 lrp- at OD420~0.3 in MOPS  (ile, val, thi) + Leu, 20 ug total RNA ,10 ug pdN6 \ PGCGROWTHCONDITIONS
\W3110 lrp- at OD420~0.3 in MOPS  (ile, val, thi) plus Leu, 20 ug total RNA, 10 ug pdN6 \ PGCGROWTHCONDITIONS
\W3110 lrp- in MOPS (ile, val, thi) to OD420~0.3, 20 ug total RNA, 10 ug pdN6\ PGCGROWTHCONDITIONS
\W3110 wt in MOPS (ile, val, thi) at OD420~0.3, 20 ug total,10 ug pdN6\ PGCGROWTHCONDITIONS
\W3110 wt OD420~0.3 in MOPS  (ile, val, thi) + Leu, 20 ug total RNA, 10 ug pdN6 \ PGCGROWTHCONDITIONS
wt + Leu vs. wt - Leu PGCGROWTHCONDITIONS
accession: U00006 PGCGROWTHCONDITIONS
Eco 50ng - 0% PGCGROWTHCONDITIONS
Eco 50ng - 10% PGCGROWTHCONDITIONS
Eco 50ng - 15% PGCGROWTHCONDITIONS
Eco 50ng - 20% PGCGROWTHCONDITIONS
Eco 50ng - 25% PGCGROWTHCONDITIONS
Eco 50ng - 32.5% PGCGROWTHCONDITIONS
Eco 50ng - 45% PGCGROWTHCONDITIONS
Eco 50ng - 5% PGCGROWTHCONDITIONS
Eco 5ng - 0% PGCGROWTHCONDITIONS
Eco 5ng - 10% PGCGROWTHCONDITIONS
Eco 5ng - 15% PGCGROWTHCONDITIONS
Eco 5ng - 20% PGCGROWTHCONDITIONS
Eco 5ng - 25% PGCGROWTHCONDITIONS
Eco 5ng - 32.5% PGCGROWTHCONDITIONS
Eco 5ng - 45% PGCGROWTHCONDITIONS
Eco 5ng - 5% PGCGROWTHCONDITIONS
E. coli was grown to mid-log phase (O.D.600nm 0.3-0.4) in Lennox LB broth (Becton Dickinson, Franklin Lakes, NJ) at 37°C. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Escherichia coli K12 wild-type PGCGROWTHCONDITIONS
Genomic DNA was extracted using Ultra Clean Soil DNA (MoBio Laboratories, Solana Beach, CA). PGCGROWTHCONDITIONS
genotype: Wild Type PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 0% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 10% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 15% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 20% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 25% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 32.5% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 45% formamide PGCGROWTHCONDITIONS
hybridization buffer (formamide content): 5% formamide PGCGROWTHCONDITIONS
hybridization buffer (total rna): 50 ng PGCGROWTHCONDITIONS
hybridization buffer (total rna): 5 ng PGCGROWTHCONDITIONS
phenotype: normal PGCGROWTHCONDITIONS
Raw data (.pair files) was analyzed using Matlab (The MathWorks, Natick, MA).  For each probe, the average intensity of three replicates were calculated after the elimination of outliers based on a standard deviation test. The average of control (Nonsense) probes was subtracted from all averages to obtain background-corrected results. PGCGROWTHCONDITIONS
R. sphaeroides was phototrophically grown to mid-log phase (100-150 kletts) in Sistrom's minimal medium (Sistrom, W. 1960. Journal of General Microbiology. 22:778-785) amended with 33.9 mM succinate . PGCGROWTHCONDITIONS
Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 108 cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
growth protocol: heat shock PGCGROWTHCONDITIONS
growth protocol: steady growth PGCGROWTHCONDITIONS
heat shock response in the minimal medium PGCGROWTHCONDITIONS
MDS42, biological rep 1 PGCGROWTHCONDITIONS
MDS42, biological rep 2 PGCGROWTHCONDITIONS
MDS42, biological rep 3 PGCGROWTHCONDITIONS
MDS42, biological rep 4 PGCGROWTHCONDITIONS
MDS42, biological rep 5 PGCGROWTHCONDITIONS
MDS42, biological rep 6 PGCGROWTHCONDITIONS
MDS42, biological rep 7 PGCGROWTHCONDITIONS
MDS42 exponentially grown in the minimal medium PGCGROWTHCONDITIONS
MDS42, heat shock, biological rep 1 PGCGROWTHCONDITIONS
MDS42, heat shock, biological rep 2 PGCGROWTHCONDITIONS
MDS42, heat shock, biological rep 3 PGCGROWTHCONDITIONS
MG1655, biological rep 1 PGCGROWTHCONDITIONS
MG1655, biological rep 2 PGCGROWTHCONDITIONS
MG1655, biological rep 3 PGCGROWTHCONDITIONS
MG1655, biological rep 4 PGCGROWTHCONDITIONS
MG1655, biological rep 5 PGCGROWTHCONDITIONS
MG1655, biological rep 6 PGCGROWTHCONDITIONS
MG1655, biological rep 7 PGCGROWTHCONDITIONS
MG1655 exponentially grown in the minimal medium PGCGROWTHCONDITIONS
MG1655, heat shock, biological rep 1 PGCGROWTHCONDITIONS
MG1655, heat shock, biological rep 2 PGCGROWTHCONDITIONS
MG1655, heat shock, biological rep 3 PGCGROWTHCONDITIONS
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). PGCGROWTHCONDITIONS
strain: MDS42 (genome reduced) PGCGROWTHCONDITIONS
strain: MG1655 (parent) PGCGROWTHCONDITIONS
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
The log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record. PGCGROWTHCONDITIONS
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg PGCGROWTHCONDITIONS
Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 20 mM EDC, pH 5.8. The crosslinking reaction was quenched with 250 mM glycine, 100 mM Tris Cl 8.0, and 4 mM NaHCO3. PGCGROWTHCONDITIONS
Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP1_AP PGCGROWTHCONDITIONS
DSP1_Total PGCGROWTHCONDITIONS
DSP2_AP PGCGROWTHCONDITIONS
DSP2_Total PGCGROWTHCONDITIONS
DSP3_AP PGCGROWTHCONDITIONS
DSP3_Total PGCGROWTHCONDITIONS
EDC1_AP PGCGROWTHCONDITIONS
EDC1_Total PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Total footprints PGCGROWTHCONDITIONS
Harvested by rapid filtration; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
Harvested by rapid filtration; DSP treated ex vivo; Total footprints PGCGROWTHCONDITIONS
Harvested by rapid filtration; EDC treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
Harvested by rapid filtration; EDC treated ex vivo; Total footprints PGCGROWTHCONDITIONS
library strategy: Ribosome profiling PGCGROWTHCONDITIONS
library strategy: Selective ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
The culture was incubated with 100 µg PGCGROWTHCONDITIONS
E. coli K12 interacted with lettuce rhizosphere rep1 PGCGROWTHCONDITIONS
E. coli K12 interacted with lettuce rhizosphere rep2 PGCGROWTHCONDITIONS
E. coli K12 interacted with lettuce rhizosphere rep3 PGCGROWTHCONDITIONS
E. coli K12 interacted with lettuce rhizosphere rep4 PGCGROWTHCONDITIONS
E. coli K12 interacted with lettuce rhizosphere rep5 PGCGROWTHCONDITIONS
E. coli K12 interacted with lettuce rhizosphere rep6 PGCGROWTHCONDITIONS
Escherichia coli MG1655 cells grown in the hydroponic system without interacting with the lettuce rhizosphere for 3 days PGCGROWTHCONDITIONS
Escherichia coli MG1655 cells interacted with the lettuce rhizosphere for 3 days PGCGROWTHCONDITIONS
Escherichia coli MG1655 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation. PGCGROWTHCONDITIONS
Signal intensities were normalized for spot and slide abnormalities with the spatial Lowess algorithm and analyzed by mixed-effect ANOVA (MAANOVA) (Kerr et al. 2000). Both Lowess and MAANOVA are part of the R PGCGROWTHCONDITIONS
Standard hot-phenol method PGCGROWTHCONDITIONS
treatment: control PGCGROWTHCONDITIONS
treatment: exposed to the lettuce rhizosphere for 3 days PGCGROWTHCONDITIONS
Cells were harvested using RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization of RNA. Stabilized cultures were used for RNA isolation using the RNeasy MiniKit system (Qiagen, Hilden, Germany). In brief, 1 ml of each culture was used and processed according to the manufacturer's instructions including an on-column DNaseI treatment. RNA quality was assayed by denaturing urea-PAGE and by measuring the ratio of absorption at 260 PGCGROWTHCONDITIONS
Data were processed using Affymetrix apt-probeset-summarize software version 1.10 and RMA algorithm. Samples were normalized using the standard normalization probes present on the Affymetrix GeneChip. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Exponential cultures of transformants were inoculated from fresh overnight cultures in LB medium supplemented with 25 µg PGCGROWTHCONDITIONS
genotype: Δ(yjjP-yjjQ-bglJ) PGCGROWTHCONDITIONS
genotype: Δ(yjjP-yjjQ-bglJ) ΔleuO PGCGROWTHCONDITIONS
genotype: Δ(yjjP-yjjQ-bglJ) ΔrcsB PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + ctrl PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 2 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 4 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pBglJ PGCGROWTHCONDITIONS
K12Δ(yjjP-yjjQ-bglJ) + pBglJ PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 2 PGCGROWTHCONDITIONS
K12Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 4 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pLeuO PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 2 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 4 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 2 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 4 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 2 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 4 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 2 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 4 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 1 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 2 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 3 PGCGROWTHCONDITIONS
K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 4 PGCGROWTHCONDITIONS
overexpression: - PGCGROWTHCONDITIONS
overexpression: BglJ PGCGROWTHCONDITIONS
overexpression: LeuO PGCGROWTHCONDITIONS
plasmid: pKEDR13 PGCGROWTHCONDITIONS
plasmid: pKESK22 PGCGROWTHCONDITIONS
plasmid: pKETS1 PGCGROWTHCONDITIONS
sample id: 1a PGCGROWTHCONDITIONS
sample id: 1b PGCGROWTHCONDITIONS
sample id: 1c PGCGROWTHCONDITIONS
sample id: 1d PGCGROWTHCONDITIONS
sample id: 2a PGCGROWTHCONDITIONS
sample id: 2b PGCGROWTHCONDITIONS
sample id: 2c PGCGROWTHCONDITIONS
sample id: 2d PGCGROWTHCONDITIONS
sample id: 3a PGCGROWTHCONDITIONS
sample id: 3b PGCGROWTHCONDITIONS
sample id: 3c PGCGROWTHCONDITIONS
sample id: 3d PGCGROWTHCONDITIONS
sample id: 4a PGCGROWTHCONDITIONS
sample id: 4b PGCGROWTHCONDITIONS
sample id: 4c PGCGROWTHCONDITIONS
sample id: 4d PGCGROWTHCONDITIONS
sample id: 5a PGCGROWTHCONDITIONS
sample id: 5b PGCGROWTHCONDITIONS
sample id: 5c PGCGROWTHCONDITIONS
sample id: 5d PGCGROWTHCONDITIONS
sample id: 6a PGCGROWTHCONDITIONS
sample id: 6b PGCGROWTHCONDITIONS
sample id: 6c PGCGROWTHCONDITIONS
sample id: 6d PGCGROWTHCONDITIONS
sample id: 7a PGCGROWTHCONDITIONS
sample id: 7b PGCGROWTHCONDITIONS
sample id: 7c PGCGROWTHCONDITIONS
sample id: 7d PGCGROWTHCONDITIONS
strain: T175 PGCGROWTHCONDITIONS
strain: T177 PGCGROWTHCONDITIONS
strain: T75 PGCGROWTHCONDITIONS
control, biological rep1 C1 PGCGROWTHCONDITIONS
control, biological rep1 C2 PGCGROWTHCONDITIONS
control, biological rep1 C3 PGCGROWTHCONDITIONS
control, biological rep2 C4 PGCGROWTHCONDITIONS
control, biological rep2 C5 PGCGROWTHCONDITIONS
control, biological rep2 C6 PGCGROWTHCONDITIONS
E.coli, grown in LB+ glycerol to0.8OD PGCGROWTHCONDITIONS
E.coli, grown in LB to0.8OD PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli was grown aerobically in Luria-Bertani (LB) broth at 30°C in an incubator shaker at 150 r.p.m. PGCGROWTHCONDITIONS
Experimental,biological rep1 G1 PGCGROWTHCONDITIONS
Experimental,biological rep1 G2 PGCGROWTHCONDITIONS
Experimental,biological rep1 G3 PGCGROWTHCONDITIONS
Experimental,biological rep2 G4 PGCGROWTHCONDITIONS
Experimental,biological rep2 G5 PGCGROWTHCONDITIONS
Experimental,biological rep2 G6 PGCGROWTHCONDITIONS
growth medium: LB+glycerol medium PGCGROWTHCONDITIONS
growth medium: LB medium PGCGROWTHCONDITIONS
RNA was isolated from the culture by using the Qiagen RNeasy mini-prep kit.cDNA was synthesized using 5-10 µg PGCGROWTHCONDITIONS
strain: Escherichia coli PGCGROWTHCONDITIONS
The intensity cell files were then imported, normalized for background correction using PLIER and data analysed using Gene Spring 11.5 software. PGCGROWTHCONDITIONS
To study gene expression in the presence and absence of glycerol, LB was supplemented with 10% (v PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 0 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 10 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 15 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 2.5 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 30 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 5 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 60 min after induction PGCGROWTHCONDITIONS
Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA). PGCGROWTHCONDITIONS
Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot PGCGROWTHCONDITIONS
EC12n090 RpoE 2.5 min Time course 4 PGCGROWTHCONDITIONS
EC12n091 RpoE 5 min Time course 4 PGCGROWTHCONDITIONS
EC12n092a RpoE 10 min Time course 4 PGCGROWTHCONDITIONS
EC12n093 RpoE 20 min Time course 4 PGCGROWTHCONDITIONS
EC12n094 RpoE 30 min Time course 4 PGCGROWTHCONDITIONS
EC12n095 RpoE 60 min Time course 4 PGCGROWTHCONDITIONS
EC12n096 RpoE 0 min Time course 4 PGCGROWTHCONDITIONS
EC12n101 RpoE 0 min Time course 3 PGCGROWTHCONDITIONS
EC7n018 RpoE 5 min Time course 1 PGCGROWTHCONDITIONS
EC7n019 RpoE 15 min Time course 1 PGCGROWTHCONDITIONS
EC7n065 RpoE 5 min Time course 2 PGCGROWTHCONDITIONS
EC7n066 RpoE 15 min Time course 2 PGCGROWTHCONDITIONS
EC7n067 RpoE 30 min Time course 2 PGCGROWTHCONDITIONS
EC7n068 RpoE 60 min Time course 2 PGCGROWTHCONDITIONS
EC7n071 RpoE 60 min Time course 1 PGCGROWTHCONDITIONS
EC8n021 RpoE 2.5 min Time course 3 PGCGROWTHCONDITIONS
EC8n022 RpoE 5 min Time course 3 PGCGROWTHCONDITIONS
EC8n050 RpoE 10min Time course 3 PGCGROWTHCONDITIONS
EC8n051 RpoE 20 min Time course 3 PGCGROWTHCONDITIONS
EC8n052 RpoE 30 min Time course 3 PGCGROWTHCONDITIONS
EC8n053 RpoE 60 min Time course 3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm PGCGROWTHCONDITIONS
MG1655 rpoHp3::lacZ delta lacX74 PGCGROWTHCONDITIONS
RpoE induced (0 min) PGCGROWTHCONDITIONS
RpoE induced (10 min) PGCGROWTHCONDITIONS
RpoE induced (15 min) PGCGROWTHCONDITIONS
RpoE induced (15min) PGCGROWTHCONDITIONS
RpoE induced (20 min) PGCGROWTHCONDITIONS
RpoE induced (2.5 min) PGCGROWTHCONDITIONS
RpoE induced (30 min) PGCGROWTHCONDITIONS
RpoE induced (5 min) PGCGROWTHCONDITIONS
RpoE induced (5min) PGCGROWTHCONDITIONS
RpoE induced (60 min) PGCGROWTHCONDITIONS
Wild type control (0 min) PGCGROWTHCONDITIONS
Wild type control (10 min) PGCGROWTHCONDITIONS
Wild type control (15 min) PGCGROWTHCONDITIONS
Wild type control (20 min) PGCGROWTHCONDITIONS
Wild type control (2.5 min) PGCGROWTHCONDITIONS
Wild type control (30 min) PGCGROWTHCONDITIONS
Wild type control (5 min) PGCGROWTHCONDITIONS
Wild type control (60 min) PGCGROWTHCONDITIONS
E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35. PGCGROWTHCONDITIONS
E_coli_transcriptome_1 PGCGROWTHCONDITIONS
E_coli_transcriptome_2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome build: E. coli [K-12 MG1655 strain (U00096.2) PGCGROWTHCONDITIONS
genotype: F-, lambda-, rph-1 PGCGROWTHCONDITIONS
reference genome: U00096.2 PGCGROWTHCONDITIONS
RNA from Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified by a standard protocol using Phenol Chloroform.  Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Epicentre, Illumina).  Then, the conventional Illumina protocol for mRNA Sequencing Sample Preparation was applied with a few modifications (see original paper). PGCGROWTHCONDITIONS
Standard Paired-End Illumina Library Construction Protocol was used with modified adapters containing optimized 20 bp barcode sequences (see original paper).  Samples with barcoded adapters were sequenced on an Illumina HiSeq 2000 with a 2x101 (for the first sequencing run) and 2x51 (for the second) base paired-end reads in one lane. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Using a combination of python (3.2.1) and bowtie(0.12.7), from the raw sequencing data, we isolated reads which contained barcode sequences that corresponded to our original list of single molecule barcodes in both forward and reverse reads for each sequence pair that had at most one mismatch. We then aligned the first 28 bases (26 bases for the second sequencing run) of the targeted sequence of both the forward and reverse reads of each cluster to the E. coli genome and kept the sequences that uniquely align fewer than three mismatches and where the two reads did not map to the same sense or antisense strand of the genome.  We used a detailed filtering process to determine the identity of closely-mapped reads. Mapped sequence fragments with a length of at least 1,000 bases were discarded.  All sequences within the same transcription unit that had the same unique tag were analyzed further. We determined that more than one sequence with the same unique tag were identical if the distance between their center positions was less than four base-pairs and if the difference in length was less than 9 base-pairs. Then for each unique sequence, we counted the number of unique barcode tags that appeared to determine the copy number of each sequence and mapped each of them to genes. We include indexed genome viewer files (.sam and .sai) for both experiments using both the conventional method and the digital method. PGCGROWTHCONDITIONS
Cells in log phase under furfural stress PGCGROWTHCONDITIONS
Cells were grown at 37°C in Luria-Bertani (LB) medium supplemented with 50 μg PGCGROWTHCONDITIONS
Data were analyzed using GeneChip Operating Software Version 1.4 (Affymetrix) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Furfural-tolerant IrrE mutant F1-37, biological rep1 PGCGROWTHCONDITIONS
Furfural-tolerant IrrE mutant F1-37, biological rep2 PGCGROWTHCONDITIONS
Furfural-tolerant IrrE mutant F1-37, biological rep3 PGCGROWTHCONDITIONS
genotype: furfural-tolerant mutant F1-37 of IrrE PGCGROWTHCONDITIONS
genotype: wild type IrrE PGCGROWTHCONDITIONS
strain: DH5a PGCGROWTHCONDITIONS
The cells were centrifuged when they reached the log phase, and then rapidly chilled and stored in liquid nitrogen until used for the DNA microarray assay PGCGROWTHCONDITIONS
Total RNA was isolated from the cells stored in liquid nitrogen using TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and RNeasy MinElute Cleanup Kits (Qiagen, Valencia, CA, USA) PGCGROWTHCONDITIONS
Wild-type IrrE, biological rep1 PGCGROWTHCONDITIONS
Wild-type IrrE, biological rep2 PGCGROWTHCONDITIONS
Wild-type IrrE, biological rep3 PGCGROWTHCONDITIONS
E_coli_negativ_control_left_chamber_rep1 PGCGROWTHCONDITIONS
E_coli_negativ_control_left_chamber_rep2 PGCGROWTHCONDITIONS
E_coli_negativ_control_left_chamber_rep3 PGCGROWTHCONDITIONS
E_coli_negativ_control_right_chamber_rep1 PGCGROWTHCONDITIONS
E_coli_negativ_control_right_chamber_rep2 PGCGROWTHCONDITIONS
E_coli_negativ_control_right_chamber_rep3 PGCGROWTHCONDITIONS
E_coli_response_control_1mM_H2O2_added_rep1 PGCGROWTHCONDITIONS
E_coli_response_control_1mM_H2O2_added_rep2 PGCGROWTHCONDITIONS
E_coli_response_control_1mM_H2O2_added_rep3 PGCGROWTHCONDITIONS
E_coli_response_control_water_added_rep1 PGCGROWTHCONDITIONS
E_coli_response_control_water_added_rep2 PGCGROWTHCONDITIONS
E_coli_response_control_water_added_rep3 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_15h_rep1 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_15h_rep2 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_15h_rep3 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_2.5h_rep1 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_2.5h_rep2 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_2.5h_rep3 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_8min_rep1 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_8min_rep2 PGCGROWTHCONDITIONS
E_coli_sham_powerline_interm_8min_rep3 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_15h_rep1 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_15h_rep2 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_15h_rep3 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_2.5h_rep1 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_2.5h_rep2 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_2.5h_rep3 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_8min_rep1 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_8min_rep2 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_cont_8min_rep3 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_interm_15h_rep1 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_interm_15h_rep2 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_interm_15h_rep3 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_interm_2.5h_rep1 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_interm_2.5h_rep2 PGCGROWTHCONDITIONS
E_coli_sham_sinusoidal_interm_2.5h_rep3 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_15h_rep1 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_15h_rep2 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_15h_rep3 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_2.5h_rep1 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_2.5h_rep2 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_2.5h_rep3 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_8min_rep1 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_8min_rep2 PGCGROWTHCONDITIONS
E_coli_treated_powerline_interm_8min_rep3 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_15h_rep1 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_15h_rep2 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_15h_rep3 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_2.5h_rep1 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_2.5h_rep2 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_2.5h_rep3 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_8min_rep1 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_8min_rep2 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_cont_8min_rep3 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_interm_15h_rep1 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_interm_15h_rep2 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_interm_15h_rep3 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_interm_2.5h_rep1 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_interm_2.5h_rep2 PGCGROWTHCONDITIONS
E_coli_treated_sinusoidal_interm_2.5h_rep3 PGCGROWTHCONDITIONS
Escherichia coli K-12 strain MG1655 was cultivated aerobically (~0.5 l PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
growth condition: steady-state continuous cultivation (dilution rate of 0.4 h-1), aerobic PGCGROWTHCONDITIONS
medium: defined mineral medium with 1 g PGCGROWTHCONDITIONS
Quality control and microarray data analysis of all 60 chips was done using R PGCGROWTHCONDITIONS
Samples of ~7.2 ml bacterial culture were mixed with 0.8 ml stop solution, pelleted and total RNA was purified using RNeasy Mini Kit (Qiagen). DNase treatment was done twice with RQ1 DNase (Promega) to remove genomic DNA. cDNA synthesis was done according to the GeneChip® Expression Analysis Technical Manual of Affymetrix using M-MLV reverse transcriptase (Promega), without DTT addition. 13 µl of EB buffer were used for elution of cDNA after its clean-up with the MiniElute CR purification Kit (Qiagen). cDNA fragmentation was done in a 20-µl reaction containing 3.5 µg cDNA, 2 µl 10x One Phor-All buffer, 2 µl DNase I (diluted to 0.2 U PGCGROWTHCONDITIONS
Samples of magnetic field-treated or sham-treated cells were withdrawn as fast as possible from the bioreactor (not later than 3 min) after the specified treatement period. Samples taken during intermittent exposure were withdrawn in the 4 min exposure break. Unexposed samples were withdrawn as fast as possible during steady-state conditions in the chemostat. In the response control experiment, samples were withdrawn 10 min after addition of 1 mM H2O2 (treated culture) or the equivalent water volume (reference culture). PGCGROWTHCONDITIONS
treatment duration: 10 min PGCGROWTHCONDITIONS
treatment duration: 15 h PGCGROWTHCONDITIONS
treatment duration: 2.5 h PGCGROWTHCONDITIONS
treatment duration: 8 min PGCGROWTHCONDITIONS
treatment duration: none PGCGROWTHCONDITIONS
treatment: sham-treated power line intermittent (2 min on, 4 min off) magnetic field PGCGROWTHCONDITIONS
treatment: sham-treated sinusoidal continous magnetic field PGCGROWTHCONDITIONS
treatment: sham-treated sinusoidal intermittent (2 min on, 4 min off) magnetic field PGCGROWTHCONDITIONS
treatment: treated power line intermittent (2 min on, 4 min off) magnetic field PGCGROWTHCONDITIONS
treatment: treated sinusoidal continous magnetic field PGCGROWTHCONDITIONS
treatment: treated sinusoidal intermittent (2 min on, 4 min off) magnetic field PGCGROWTHCONDITIONS
treatment: unexposed, left chamber PGCGROWTHCONDITIONS
treatment: unexposed, right chamber PGCGROWTHCONDITIONS
treatment: unexposed, treated with 1mM H2O2 PGCGROWTHCONDITIONS
treatment: unexposed, treated with water PGCGROWTHCONDITIONS
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press) PGCGROWTHCONDITIONS
E. coli recoded ompF PGCGROWTHCONDITIONS
E. coli recoded ompF (recoded ompF gene) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
medium: MOPS PGCGROWTHCONDITIONS
OmpFrecode_f.wig: NC_000913.2 PGCGROWTHCONDITIONS
OmpFrecode_r.wig: NC_000913.2 PGCGROWTHCONDITIONS
Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BJW9 w PGCGROWTHCONDITIONS
treatment: Ribosome-protected mRNA, Ribosome footprint sample digested with 60 units of micrococcal nuclease per A260 absorbance PGCGROWTHCONDITIONS
aerobic reference PGCGROWTHCONDITIONS
anaerobic reference PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
fnr- aerobic PGCGROWTHCONDITIONS
fnr- aerobic  AN rep 1 PGCGROWTHCONDITIONS
fnr- aerobic  AN rep 2 PGCGROWTHCONDITIONS
fnr- aerobic  AN rep 3 PGCGROWTHCONDITIONS
fnr- aerobic rep 1 PGCGROWTHCONDITIONS
fnr- aerobic rep 2 PGCGROWTHCONDITIONS
fnr- aerobic rep 3 PGCGROWTHCONDITIONS
fnr- anaerobic PGCGROWTHCONDITIONS
fnr- anaerobic  AN rep 1 PGCGROWTHCONDITIONS
fnr- anaerobic  AN rep 2 PGCGROWTHCONDITIONS
fnr- anaerobic  AN rep 3 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2  PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2  AN rep 1 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2  AN rep 2 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2  AN rep 3 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2 rep 1 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2 rep 2 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO2 rep 3 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3  AN rep 1 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3  AN rep 2 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3  AN rep 3 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3 rep 1 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3 rep 2 PGCGROWTHCONDITIONS
fnr- anaerobic plus NO3 rep 3 PGCGROWTHCONDITIONS
fnr- anaerobic rep 1 PGCGROWTHCONDITIONS
fnr- anaerobic rep 2 PGCGROWTHCONDITIONS
fnr- anaerobic rep 3 PGCGROWTHCONDITIONS
Genetic background: fnr- PGCGROWTHCONDITIONS
Genetic background:wt PGCGROWTHCONDITIONS
Genetic background: wt PGCGROWTHCONDITIONS
Genetic background: wtGrowth conditions: aerobic PGCGROWTHCONDITIONS
Growth conditions: aaerobic PGCGROWTHCONDITIONS
Growth conditions: aerobic PGCGROWTHCONDITIONS
Growth conditions: anaerobic PGCGROWTHCONDITIONS
Growth conditions: anaerobic plus NO2 PGCGROWTHCONDITIONS
Growth conditions: anaerobic plus NO3 PGCGROWTHCONDITIONS
narXL anaerobic plus NO2 PGCGROWTHCONDITIONS
narXLP anaerobic plus NO2 PGCGROWTHCONDITIONS
narXLP rep 1 PGCGROWTHCONDITIONS
narXLP rep 2 PGCGROWTHCONDITIONS
narXLP rep 3 PGCGROWTHCONDITIONS
narXL rep 1 PGCGROWTHCONDITIONS
narXL rep 2 PGCGROWTHCONDITIONS
narXL rep 3 PGCGROWTHCONDITIONS
narXL rep 4 PGCGROWTHCONDITIONS
Raw, not normalised PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655 PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: fnr-, Growth conditions: aerobic PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: fnr-, Growth conditions: anaerobic PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: fnr-, Growth conditions: anaerobic plus NO2 PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: fnr-, Growth conditions: anaerobic plus NO3 PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: narXL, Growth conditions: anaerobic plus NO2 PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: narXLP, Growth conditions: anaerobic plus NO2 PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: wt, Growth conditions: aerobic PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: wt, Growth conditions: anaerobic PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: wt, Growth conditions: anaerobic plus NO2 PGCGROWTHCONDITIONS
Strain:E.coli K-12 MG1655, Genetic background: wt, Growth conditions: anaerobic plus NO3 PGCGROWTHCONDITIONS
wt aerobic PGCGROWTHCONDITIONS
wt aerobic  AN rep 1 PGCGROWTHCONDITIONS
wt aerobic  AN rep 2 PGCGROWTHCONDITIONS
wt aerobic  AN rep 3 PGCGROWTHCONDITIONS
wt aerobic rep 1 PGCGROWTHCONDITIONS
wt aerobic rep 2 PGCGROWTHCONDITIONS
wt aerobic rep 3 PGCGROWTHCONDITIONS
wt anaerobic PGCGROWTHCONDITIONS
wt anaerobic  PGCGROWTHCONDITIONS
wt anaerobic  AN rep 1 PGCGROWTHCONDITIONS
wt anaerobic  AN rep 2 PGCGROWTHCONDITIONS
wt anaerobic  AN rep 3 PGCGROWTHCONDITIONS
wt anaerobic plus NO2 PGCGROWTHCONDITIONS
wt anaerobic plus NO2  AN rep 1 PGCGROWTHCONDITIONS
wt anaerobic plus NO2  AN rep 2 PGCGROWTHCONDITIONS
wt anaerobic plus NO2  AN rep 3 PGCGROWTHCONDITIONS
wt anaerobic plus NO2 rep 1 PGCGROWTHCONDITIONS
wt anaerobic plus NO2 rep 2 PGCGROWTHCONDITIONS
wt anaerobic plus NO2 rep 3 PGCGROWTHCONDITIONS
wt anaerobic plus NO3 PGCGROWTHCONDITIONS
wt anaerobic plus NO3  AN rep 1 PGCGROWTHCONDITIONS
wt anaerobic plus NO3  AN rep 2 PGCGROWTHCONDITIONS
wt anaerobic plus NO3  AN rep 3 PGCGROWTHCONDITIONS
wt anaerobic plus NO3 rep 1 PGCGROWTHCONDITIONS
wt anaerobic plus NO3 rep 2 PGCGROWTHCONDITIONS
wt anaerobic plus NO3 rep 3 PGCGROWTHCONDITIONS
wt anaerobic rep 1 PGCGROWTHCONDITIONS
wt anaerobic rep 2 PGCGROWTHCONDITIONS
wt anaerobic rep 3 PGCGROWTHCONDITIONS
A 5ml overnight culture of E. coli O157:H7 (Sakai) was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg PGCGROWTHCONDITIONS
A 5ml overnight culture of E. coli O157:H7 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg PGCGROWTHCONDITIONS
A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Brunswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg PGCGROWTHCONDITIONS
A 5ml overnight culture of MG1655 was grown in Neidhardt's EZ Rich Defined Medium for 18 h at 37C. The culture was diluted 1:100 into 50 ml of fresh, prewarmed Neidhardt's EZ Rich Defined Medium in a 125 ml Ehrlenmeyer flask and shaken at 37C, 150 rpm in a New Bruswick Shaking water bath until the culture density reached 0.4. Half of the culture was transferred to a second identical flask containing menadione bisulphite to a final concentration of 0.5 mg PGCGROWTHCONDITIONS
An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions. Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd). The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom). PGCGROWTHCONDITIONS
E. coli K-12 untreated (reference sample)_rep #1 PGCGROWTHCONDITIONS
E. coli K-12 untreated (reference sample)_rep #2 PGCGROWTHCONDITIONS
E. coli K-12 untreated (reference sample)_rep #3 PGCGROWTHCONDITIONS
E. coli O157 (Sakai) untreated (reference sample)_rep #1 PGCGROWTHCONDITIONS
E. coli O157 (Sakai) untreated (reference sample)_rep #2 PGCGROWTHCONDITIONS
E. coli O157 (Sakai) untreated (reference sample)_rep #3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli K-12 treated with menadione_rep#1 PGCGROWTHCONDITIONS
Escherichia coli K-12 treated with menadione_rep #2 PGCGROWTHCONDITIONS
Escherichia coli K-12 treated with menadione_rep #3 PGCGROWTHCONDITIONS
Escherichia coli O157 (Sakai) treated with menadione_rep#1 PGCGROWTHCONDITIONS
Escherichia coli O157 (Sakai) treated with menadione_rep#2 PGCGROWTHCONDITIONS
Escherichia coli O157 (Sakai) treated with menadione_rep#3 PGCGROWTHCONDITIONS
GenePix software (Axon Instruments, Union City, CA) version 5.1 was used to process the scanned data and generate the gpr files. PGCGROWTHCONDITIONS
medium: Neidhardt's EZ Rich Defined Medium (Teknova, USA) PGCGROWTHCONDITIONS
od600: 0.4 PGCGROWTHCONDITIONS
Oxidative stress in E. coli K-12 #1 PGCGROWTHCONDITIONS
Oxidative stress in E. coli K-12 #2 PGCGROWTHCONDITIONS
Oxidative stress in E. coli K-12 #3 PGCGROWTHCONDITIONS
Oxidative stress in E. coli O157 (Sakai) #1 PGCGROWTHCONDITIONS
Oxidative stress in E. coli O157 (Sakai) #2 PGCGROWTHCONDITIONS
Oxidative stress in E. coli O157 (Sakai) #3 PGCGROWTHCONDITIONS
strain: k-12 MG1655 wild-type PGCGROWTHCONDITIONS
strain: o157: H7 (Sakai) wild-type PGCGROWTHCONDITIONS
treatment: 0.5 mg PGCGROWTHCONDITIONS
ampicilin treatment PGCGROWTHCONDITIONS
Ampicilin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1 PGCGROWTHCONDITIONS
Amp_Treatment_genomemappedreads_statistical_output.txt: NC_000913.2 PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase with ampicilin treatment PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase with florfenicol treatment PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase with streptomycin treatment PGCGROWTHCONDITIONS
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http: PGCGROWTHCONDITIONS
Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing. PGCGROWTHCONDITIONS
E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
florfenicol treatment PGCGROWTHCONDITIONS
Florfenicol_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1 PGCGROWTHCONDITIONS
Flor_treatment_genomemappedreads_statistical_output.txt: NC_000913.2 PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
no treatment PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: DH5α(pAR060302) PGCGROWTHCONDITIONS
streptomycin treatment PGCGROWTHCONDITIONS
Streptomycin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1 PGCGROWTHCONDITIONS
Strep_treatment_genomemappedreads_statistical_output.txt: NC_000913.2 PGCGROWTHCONDITIONS
treatment: ampicillin (50 µg PGCGROWTHCONDITIONS
treatment: florfenicol (30 µg PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
treatment: streptomycin (50 µg PGCGROWTHCONDITIONS
E. coli O157:H7 interacted with lettuce rhizosphere biological rep 1 slide 1 PGCGROWTHCONDITIONS
E. coli O157:H7 interacted with lettuce rhizosphere biological rep 1 slide 2 PGCGROWTHCONDITIONS
E. coli O157:H7 interacted with lettuce rhizosphere biological rep 2 slide 3 PGCGROWTHCONDITIONS
E. coli O157:H7 interacted with lettuce rhizosphere biological rep 2 slide 4 PGCGROWTHCONDITIONS
E. coli O157:H7 interacted with lettuce rhizosphere biological rep 3 slide 5 PGCGROWTHCONDITIONS
E. coli O157:H7 interacted with lettuce rhizosphere biological rep 3 slide 6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli EDL 933 cells grown in the hydroponic system without interacting with the lettuce rhizosphere for 3 days PGCGROWTHCONDITIONS
Escherichia coli EDL 933 cells interacted with the lettuce rhizosphere for 3 days PGCGROWTHCONDITIONS
Escherichia coli EDL 933 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells PGCGROWTHCONDITIONS
Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation. PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Signal intensities were normalized for spot and slide abnormalities with the spatial Lowess algorithm and analyzed by mixed-effect ANOVA (MAANOVA) (Kerr et al. 2000). Both Lowess and MAANOVA are part of the R PGCGROWTHCONDITIONS
Standard hot-phenol method PGCGROWTHCONDITIONS
strain: O157: H7 PGCGROWTHCONDITIONS
treatment: grown in lettuce rhizosphere PGCGROWTHCONDITIONS
treatment: grown without lettuce rhizosphere PGCGROWTHCONDITIONS
control sample at 30 min, biological rep1 PGCGROWTHCONDITIONS
control sample at 30 min, biological rep2 PGCGROWTHCONDITIONS
control sample at 60 min, biological rep1 PGCGROWTHCONDITIONS
control sample at 60 min, biological rep2 PGCGROWTHCONDITIONS
Data were normalized using RMA algorithm from R PGCGROWTHCONDITIONS
Escherichia coli MG1655 after 30 min incubation PGCGROWTHCONDITIONS
Escherichia coli MG1655 after 30 min incubation following colicin M treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 after 60 min incubation PGCGROWTHCONDITIONS
Escherichia coli MG1655 after 60 min incubation following colicin M treatment PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Overnight cultures of E. coli MG1655  grown at 37°C with shaking at 200 rpm were diluted 1:625 into 50 ml of LB broth (Roth), and incubated at 37°C with shaking at 200 rpm. PGCGROWTHCONDITIONS
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. PGCGROWTHCONDITIONS
treated sample at 30 min, biological rep1 PGCGROWTHCONDITIONS
treated sample at 30 min, biological rep2 PGCGROWTHCONDITIONS
treated sample at 60 min, biological rep1 PGCGROWTHCONDITIONS
treated sample at 60 min, biological rep2 PGCGROWTHCONDITIONS
treatment: treated culture PGCGROWTHCONDITIONS
treatment: untreated culture PGCGROWTHCONDITIONS
When the cultures reached an OD600 0.6 they were split into two flasks, each containing 20 ml of the culture. One was treated with a subinhibitory concentration of purified colicin M, while the untreated served as a control. 2-ml culture aliquotes were harvested from each flask after 30 min and 60 min incubation at 37°C  and were mixed with 4 ml RNAProtect Bacteria Reagent (Qiagen). PGCGROWTHCONDITIONS
Bacterial pellets were resuspended in 350µl RNAwiz  (Ambion, Austin, TX) and kept at -80 °C. PGCGROWTHCONDITIONS
Data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation. The EB (Wright and Simon) test was used for the fold change and the p­value calculation, PGCGROWTHCONDITIONS
E. coli O157:H7 was grown in 15mL falcon tubes containing 8mL of filtered rat's caecal content. Growth were performed in static condition at 37 °C for 6 hours. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 cultivated for 6 hours in the caecal content of rats PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Germfree rat's caecum, biological rep1 PGCGROWTHCONDITIONS
Germfree rat's caecum, biological rep2 PGCGROWTHCONDITIONS
Germfree rat's caecum, biological rep3 PGCGROWTHCONDITIONS
growth protocol: control PGCGROWTHCONDITIONS
growth protocol: in the caecal content of rats associated with the human microbiota PGCGROWTHCONDITIONS
Human intestinal microbiota associated rat's caecum, biological rep1 PGCGROWTHCONDITIONS
Human intestinal microbiota associated rat's caecum, biological rep2 PGCGROWTHCONDITIONS
Human intestinal microbiota associated rat's caecum, biological rep3 PGCGROWTHCONDITIONS
RNA extractions were performed using RiboPure™­Bacteria Kit (Ambion, Austin, TX), according to the manufacturer's recommendations PGCGROWTHCONDITIONS
Agilent Feature Extraction Software v. 9.5.3.1  was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
control PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli control vs H2O2 Rep1 PGCGROWTHCONDITIONS
Escherichia coli control vs H2O2 Rep2 PGCGROWTHCONDITIONS
H2O2 PGCGROWTHCONDITIONS
One conditions: 1% (v PGCGROWTHCONDITIONS
Overnight culture of E. coli W3110 in LB was diluted in M9 minimal medium with supplements to OD600=0.01 and was incubated at 37 Ceilsus degree witouth shaking until its OD600 reached 0.1. PGCGROWTHCONDITIONS
strain: K-12 W3110 PGCGROWTHCONDITIONS
Total RNA was extracted from 5ml cell culture at 10min incubation with or without 1% Hydrogen peroxide using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol PGCGROWTHCONDITIONS
treatment: 1% H202, anaerobic PGCGROWTHCONDITIONS
treatment: 1% H2O2, anaerobic PGCGROWTHCONDITIONS
treatment: control, anaerobic PGCGROWTHCONDITIONS
Agilent Feature Extraction Software v. 9.5.3.1  was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli wild type vs luxS mutants with 10% H2O2 Rep1 PGCGROWTHCONDITIONS
Escherichia coli wild type vs luxS mutants with 10% H2O2 Rep2 PGCGROWTHCONDITIONS
Escherichia coli wild type vs luxS mutants with 30% H2O2 Rep1 PGCGROWTHCONDITIONS
Escherichia coli wild type vs luxS mutants with 30% H2O2 Rep2 PGCGROWTHCONDITIONS
Escherichia coli wild type vs luxS mutants without H2O2 Rep1 PGCGROWTHCONDITIONS
Escherichia coli wild type vs luxS mutants without H2O2 Rep2 PGCGROWTHCONDITIONS
genotype: luxS PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
luxS mutants, 10% H2O2 PGCGROWTHCONDITIONS
luxS mutants, 30% H2O2 PGCGROWTHCONDITIONS
luxS mutants, without H2O2 PGCGROWTHCONDITIONS
Overnight culture of E. coli in LB was diluted in LB supplemented with 0.8% glucose to OD600=0.02 and was continuously incubated at 30 degree celcius with shaking until its OD600 reached 1.0 PGCGROWTHCONDITIONS
strain: K-12 W3110 PGCGROWTHCONDITIONS
three different concentrations, without H2O2, 10% (v PGCGROWTHCONDITIONS
Total RNA was extracted from 5ml cell culture after 30min incubation with or without H2O2 treatment using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol PGCGROWTHCONDITIONS
treatment: 10% H202 PGCGROWTHCONDITIONS
treatment: 30% H202 PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
wild type, 10% H2O2 PGCGROWTHCONDITIONS
wild type, 30% H2O2 PGCGROWTHCONDITIONS
wild type, without H2O2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
JCB570 PGCGROWTHCONDITIONS
JQ004 (rraA) PGCGROWTHCONDITIONS
rraA deletion, OD600=0.3 PGCGROWTHCONDITIONS
rraA deletion, OD600=0.5 PGCGROWTHCONDITIONS
rraA deletion, OD600=1.0 PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
KSL2000, 0.1 % arabinose PGCGROWTHCONDITIONS
KSL2000, no arabinose PGCGROWTHCONDITIONS
KSL2000 plus pTrc99A PGCGROWTHCONDITIONS
KSL2000 plus pTrc99A-RraA PGCGROWTHCONDITIONS
KSL2000-Rne depletion PGCGROWTHCONDITIONS
KSL2000-RraA overexpression PGCGROWTHCONDITIONS
KSL2009, 0.1% arabinose PGCGROWTHCONDITIONS
KSL2009, no arabinose PGCGROWTHCONDITIONS
KSL2009-N-Rne depletion PGCGROWTHCONDITIONS
KSL2009 plus pTrc99A PGCGROWTHCONDITIONS
KSL2009 plus pTrc99A-RraA PGCGROWTHCONDITIONS
KSL2009-RraA overexpression PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
Escherichia coli O157 PGCGROWTHCONDITIONS
genetic background: O157 H19 PGCGROWTHCONDITIONS
genotype: triclosan tolerant mutant PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Microarray analysis including pre-processing, normalisation anmd statistical analysis were performed using R (R, 2007) version 2.6 and Bioconductor (Gentleman et al. 2004, Genome Biol. 5:R80) version 2.1 as previously described by Morris et al.(2009, Physiol. Genomics 39:28-37). Propagating uncertainty in microarray analysis (puma) method was used to estimate fold changes and P-like values of differential gene expression analysis (Pearson et al. 2009, BMC Bioinformatics 10:211). PGCGROWTHCONDITIONS
Mutant E. coli O157 treated with 6 ug PGCGROWTHCONDITIONS
Mutant E. coli O157 untreated, biological rep 1 PGCGROWTHCONDITIONS
Mutant E. coli O157 untreated, biological rep 2 PGCGROWTHCONDITIONS
Mutant E. coli O157 untreated, biological rep 3 PGCGROWTHCONDITIONS
strain: T3 5H5 PGCGROWTHCONDITIONS
strain: T3 5H5 M PGCGROWTHCONDITIONS
The subculture was split into two 10 ml portions, one of which was treated with 6ug PGCGROWTHCONDITIONS
The wildtype and mutant E. coli O157:H19 strains were grown on LB agar incubated at 37c x 24h. A single isolated colony for each strain was selected and inoculated into 20 ml LB broth and incubated at 37c until growth reached an optical density of 0.6 at 600nm. PGCGROWTHCONDITIONS
Total RNA was stabilised and subsequently purified from a 500 ul portion of each bacterial culture using a RNAprotect Bacterial Reagent Mini Kit (Qiagen, Crawley, UK) PGCGROWTHCONDITIONS
treatment: triclosan PGCGROWTHCONDITIONS
treatment: untreated PGCGROWTHCONDITIONS
Triclosan tolerant mutant triclosan treated biological rep 1 PGCGROWTHCONDITIONS
Triclosan tolerant mutant triclosan treated biological rep 2 PGCGROWTHCONDITIONS
Triclosan tolerant mutant triclosan treated biological rep 3 PGCGROWTHCONDITIONS
Triclosan tolerant mutant untreated biological rep 1 PGCGROWTHCONDITIONS
Triclosan tolerant mutant untreated biological rep 2 PGCGROWTHCONDITIONS
Triclosan tolerant mutant untreated biological rep 3 PGCGROWTHCONDITIONS
Wildtype E. coli O157 treated with 6 ug PGCGROWTHCONDITIONS
Wildtype E. coli O157 untreated, biological rep 1 PGCGROWTHCONDITIONS
Wildtype E. coli O157 untreated, biological rep 2 PGCGROWTHCONDITIONS
Wildtype E. coli O157 untreated, biological rep 3 PGCGROWTHCONDITIONS
Wildtype triclosan treated biological rep 1 PGCGROWTHCONDITIONS
Wildtype triclosan treated biological rep 2 PGCGROWTHCONDITIONS
Wildtype triclosan treated biological rep 3 PGCGROWTHCONDITIONS
Wildtype untreated biological rep 1 PGCGROWTHCONDITIONS
Wildtype untreated biological rep 2 PGCGROWTHCONDITIONS
Wildtype untreated biological rep 3 PGCGROWTHCONDITIONS
0.5MIC of CYA, biological rep1 PGCGROWTHCONDITIONS
0.5MIC of CYA, biological rep2 PGCGROWTHCONDITIONS
0.5MIC of CYA, biological rep3 PGCGROWTHCONDITIONS
Cells were grown in  anaerobic incubator for 1h at 37℃ and drugs were added according to the different concentrations. The cultures were incubated for 30min. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli treated with 0.5MIC of cyadox PGCGROWTHCONDITIONS
Escherichia coli treated with 1%DMSO PGCGROWTHCONDITIONS
Escherichia coli treated with MBC of cyadox PGCGROWTHCONDITIONS
Escherichia coli treated with MBC of olaquindox PGCGROWTHCONDITIONS
Escherichia coli treated with MIC of olaquindox PGCGROWTHCONDITIONS
MBC of CYA, biological rep1 PGCGROWTHCONDITIONS
MBC of CYA, biological rep2 PGCGROWTHCONDITIONS
MBC of CYA, biological rep3 PGCGROWTHCONDITIONS
MBC of OLA, biological rep1 PGCGROWTHCONDITIONS
MBC of OLA, biological rep2 PGCGROWTHCONDITIONS
MBC of OLA, biological rep3 PGCGROWTHCONDITIONS
MIC of OLA, biological rep1 PGCGROWTHCONDITIONS
MIC of OLA, biological rep2 PGCGROWTHCONDITIONS
MIC of OLA, biological rep3 PGCGROWTHCONDITIONS
Solvent control, biological rep1 PGCGROWTHCONDITIONS
Solvent control, biological rep2 PGCGROWTHCONDITIONS
Solvent control, biological rep3 PGCGROWTHCONDITIONS
strain: CVCC2943 PGCGROWTHCONDITIONS
The cells were centrifuged at 8000 rpm for 5min at 4°C. The cell pellets were snap-frozen in liquid nitrogen and kept at -80°C PGCGROWTHCONDITIONS
The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method. PGCGROWTHCONDITIONS
Trizol extraction of total RNA was performed according to the manufacturer's instructions. PGCGROWTHCONDITIONS
Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Eno- (DF261) in M9 + 0.2% Glycerol, 0.2% Tryptone, 40mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
N-RNaseE (BZ453)  in   M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Pnp- (YHC012)  in  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Pnp- (YHC012)) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
RhlB- (SU02)  in  M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
RhlB- (SU02)  in  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
RhlB- (SU02)  in  M9 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
RhlB- (SU02) in   M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
Wild Type (K10)  M9 + 0.2% Glycerol, 0.2% Tryptone, 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Wild Type (K10)  M9 + 0.2% Glycerol, 0.2% Tryptone, 40 mM Suc. at 30 CMid Log PGCGROWTHCONDITIONS
Wild Type (K10)  M9 0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Wild Type (N3433)  in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Wild Type (N3433)  M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Wild Type (N3433)  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
WT (K10) vs Eno- (DF261) in M9 + 0.2% Glycerol, 0.2% Tryptone, 40 mM Suc. at 30 C Mid Log Trial A PGCGROWTHCONDITIONS
WT (K10) vs Eno- (DF261) in M9  0.2% Glycerol, 0.2% Tryptone, 40 mM Suc. at 30 C Mid Log Trial B PGCGROWTHCONDITIONS
WT (K10) vs Eno- (DF261)  M9 + 0.2% Glycerol,  0.2% Tryptone, 40 mM Suc. at 30 C Mid Log Trial A1 PGCGROWTHCONDITIONS
WT (K10) vs Eno- (DF261)  M9 + 0.2% Glycerol, 0.2% Tryptone, 40 mM Suc. at 30 C Mid Log Trial B1 PGCGROWTHCONDITIONS
WT (N3433) vs Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial A2 PGCGROWTHCONDITIONS
WT (N3433) vs Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial B2 PGCGROWTHCONDITIONS
WT (N3433) vs Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial C2 PGCGROWTHCONDITIONS
WT (N3433) vs RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial A PGCGROWTHCONDITIONS
WT (N3433) vs RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial A1 PGCGROWTHCONDITIONS
WT (N3433) vs RhlB- (SU02) in M9 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial B PGCGROWTHCONDITIONS
WT (N3433) vs RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial B1 PGCGROWTHCONDITIONS
WT (N3433) vs RhlB- (SU02) in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial C PGCGROWTHCONDITIONS
WT (N3433) vs RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial C1 PGCGROWTHCONDITIONS
WT (SH3208)  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
WT (SH3208) vs N-RNaseE (BZ453)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
WT (SH3208) vs N-RNaseE (BZ453)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial A PGCGROWTHCONDITIONS
WT (SH3208) vs N-RNaseE (BZ453)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial B PGCGROWTHCONDITIONS
WT (SH3208) vs N-RNaseE (BZ453)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Trial C PGCGROWTHCONDITIONS
1.5' RNA Decay N-RNaseE (BZ453) in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A PGCGROWTHCONDITIONS
1.5' RNA Decay N-RNaseE (BZ453)  in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A1 PGCGROWTHCONDITIONS
1.5' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. B PGCGROWTHCONDITIONS
1.5' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. B1 PGCGROWTHCONDITIONS
1.5' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone, 40 mM Suc.at 30 C Mid Log Rep A PGCGROWTHCONDITIONS
1.5' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log Rep B PGCGROWTHCONDITIONS
1.5' RNA Decay of Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A2 PGCGROWTHCONDITIONS
1.5' RNA Decay of Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. B2 PGCGROWTHCONDITIONS
1.5' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate A PGCGROWTHCONDITIONS
1.5' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate A1 PGCGROWTHCONDITIONS
1.5' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate B PGCGROWTHCONDITIONS
1.5' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate B1 PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (K10) in M9  0.2% Glycerol 0.2% Tryptone, 40 mM Suc. at 30 C Mid Log Rep A PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc.at 30 C Mid Log Rep B PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (N3433) in M9  0.2% Glycerol 0.2% Tryptone at 30 C Mid Log Rep. A2 PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (N3433) in M9  0.2% Glycerol 0.2% Tryptone at 30 C Mid Log Rep. B2 PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (N3433) in M9  0.2% Glycerol 0.2% Tryptone at 30 C Mid Log Replicate A1 PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate B1 PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (SH3208) in M9  0.2% Glycerol 0.2% Tryptone at 30 C Mid Log Rep. A1 PGCGROWTHCONDITIONS
1.5' RNA Decay of WT (SH3208) in M9  0.2% Glycerol 0.2% Tryptone at 30 C Mid Log Rep. B1 PGCGROWTHCONDITIONS
3' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
3' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1 PGCGROWTHCONDITIONS
3' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log Rep A PGCGROWTHCONDITIONS
3' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone at 40 mM Suc. 30  C Mid Log Rep B PGCGROWTHCONDITIONS
3' RNA Decay of Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 2 PGCGROWTHCONDITIONS
3' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
3' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log1 PGCGROWTHCONDITIONS
3' RNA Decay of WT (K10) in M9 0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
3' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log1 PGCGROWTHCONDITIONS
3' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 2 PGCGROWTHCONDITIONS
3' RNA Decay of WT (SH3208) in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1 PGCGROWTHCONDITIONS
4.5' RNA Decay N-RNaseE (BZ453)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
4.5' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1 PGCGROWTHCONDITIONS
4.5' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30  C Mid Log PGCGROWTHCONDITIONS
4.5' RNA Decay of Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 2 PGCGROWTHCONDITIONS
4.5' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
4.5' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log1 PGCGROWTHCONDITIONS
4.5' RNA Decay of WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
4.5' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log1 PGCGROWTHCONDITIONS
4.5' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 2 PGCGROWTHCONDITIONS
4.5' RNA Decay of WT (SH3208) in M9  0.2% Glycerol, .2% Tryptone at 30 C Mid Log 1 PGCGROWTHCONDITIONS
6' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A PGCGROWTHCONDITIONS
6' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A1 PGCGROWTHCONDITIONS
6' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. B PGCGROWTHCONDITIONS
6' RNA Decay N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. B1 PGCGROWTHCONDITIONS
6' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30  C Mid Log Rep A PGCGROWTHCONDITIONS
6' RNA Decay of Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30  C Mid Log Rep B PGCGROWTHCONDITIONS
6' RNA Decay of Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. A2 PGCGROWTHCONDITIONS
6' RNA Decay of Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep. B2 PGCGROWTHCONDITIONS
6' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate A PGCGROWTHCONDITIONS
6' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate A1 PGCGROWTHCONDITIONS
6' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate B PGCGROWTHCONDITIONS
6' RNA Decay of RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate B1 PGCGROWTHCONDITIONS
6' RNA Decay of WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30  C Mid Log Rep A PGCGROWTHCONDITIONS
6' RNA Decay of WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30  C Mid Log Rep B PGCGROWTHCONDITIONS
6' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep A2 PGCGROWTHCONDITIONS
6' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate A1 PGCGROWTHCONDITIONS
6' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Replicate B1 PGCGROWTHCONDITIONS
6' RNA Decay of WT (N3433) in M9 + 0.2% Glycerol, .2% Tryptone at 30 C Mid Log Rep B2 PGCGROWTHCONDITIONS
6' RNA Decay of WT (SH3208) in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep A1 PGCGROWTHCONDITIONS
6' RNA Decay of WT (SH3208) in M9  0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log Rep B1 PGCGROWTHCONDITIONS
Eno- (DF261)  in  M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Eno- (DF261) in  M9  0.2% Glycerol  0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Eno- (DF261) in  M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40mM Suc. at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40mM Suc. at 30 C Mid Log 3.0' post rif PGCGROWTHCONDITIONS
Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40mM Suc. at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
Eno- (DF261) in M9  0.2% Glycerol 0.2% Tryptone 40mM Suc. at 30 C Mid Log 6.0' post rif PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
N-RNaseE (BZ453)  in   M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
N-RNaseE (BZ453)  in  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in   M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
N-RNaseE (BZ453)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
N-RNaseE (BZ453) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif PGCGROWTHCONDITIONS
Pnp- (YHC012) in   M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Pnp- (YHC012) in  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
Pnp- (YHC012) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif PGCGROWTHCONDITIONS
RhlB- (SU02) in  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
RhlB- (SU02)  in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif PGCGROWTHCONDITIONS
RhlB- (SU02) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 Mid Log 6' post rif PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 0C Mid Log 6.0' post rif PGCGROWTHCONDITIONS
WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
WT (K10) in M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log 6.0' post rif PGCGROWTHCONDITIONS
WT (K10)  M9  0.2% Glycerol 0.2% Tryptone 40 mM Suc. at 30 C Mid Log PGCGROWTHCONDITIONS
WT (K10)  M9  0.2% Glycerol 0.2% Tryptone 40 mM Succinate at 30 C Mid Log PGCGROWTHCONDITIONS
WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3.0' post rif PGCGROWTHCONDITIONS
WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
WT (N3433) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif PGCGROWTHCONDITIONS
WT (N3433)  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
WT (N3433) M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif PGCGROWTHCONDITIONS
WT (SH3208) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
WT (SH3208) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 1.5' post rif PGCGROWTHCONDITIONS
WT (SH3208) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 3' post rif PGCGROWTHCONDITIONS
WT (SH3208) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 4.5' post rif PGCGROWTHCONDITIONS
WT (SH3208) in M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log 6' post rif PGCGROWTHCONDITIONS
WT (SH3208)  M9 + 0.2% Glycerol, 0.2% Tryptone at 30 C Mid Log PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol PGCGROWTHCONDITIONS
B500_1 PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 1 PGCGROWTHCONDITIONS
biological replicate: 2 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G500_1 PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
H500_1 PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
O500_1 PGCGROWTHCONDITIONS
O500_2 PGCGROWTHCONDITIONS
P500_1 PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: acidic PGCGROWTHCONDITIONS
stress: Minimal medium PGCGROWTHCONDITIONS
stress: n-butanol PGCGROWTHCONDITIONS
stress: osmotic PGCGROWTHCONDITIONS
stress: oxidative PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
After reaching an OD600nm of 0.9, cell cultures were placed immediately in a shaking water bath along with another BHI flask carrying a type T thermocouple connected to a MultiPaq 21 datalogger (Datapaq Inc.) for temperature profile and the process lethality values monitoring in real time. Bacteria suspension were heated at 58°C to process lethality values of 2 and 3, at 60°C to a process lethality value of 3, or until a temperature of 71°C was reached. Just after heating, cell suspension was cooled in an iced water bath under constant agitation (150 rpm) until the temperature dropped back to no less than 37°C in order to avoid cold stress. Cell suspensions were then centrifuged and the remaining cell pellets were treated with RNA protect bacteria reagent (Qiagen Inc.) prior to freezing at -80°C. PGCGROWTHCONDITIONS
Bacteria at 58°C F = 2 PGCGROWTHCONDITIONS
Bacteria at 58°C F = 3 PGCGROWTHCONDITIONS
Bacteria at 60°C F = 3 PGCGROWTHCONDITIONS
Bacteria at 71°C PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 1 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 2 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 3 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 4 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 2 - Replicate 5 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 1 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 2 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 3 PGCGROWTHCONDITIONS
Bacteria suspension heated at 58°C to a process lethality value of 3 - Replicate 4 PGCGROWTHCONDITIONS
Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 1 PGCGROWTHCONDITIONS
Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 2 PGCGROWTHCONDITIONS
Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 3 PGCGROWTHCONDITIONS
Bacteria suspension heated at 60°C to a process lethality value of 3 - Replicate 4 PGCGROWTHCONDITIONS
Bacteria suspension heated to a core temperature of 71°C                - Replicate 1 PGCGROWTHCONDITIONS
Bacteria suspension heated to a core temperature of 71°C                - Replicate 2 PGCGROWTHCONDITIONS
Bacteria suspension heated to a core temperature of 71°C                - Replicate 3 PGCGROWTHCONDITIONS
Bacteria suspension heated to a core temperature of 71°C                - Replicate 4 PGCGROWTHCONDITIONS
Bacteria suspension heated to a core temperature of 71°C                - Replicate 5 PGCGROWTHCONDITIONS
Control bacteria at 37°C (common reference).  Total RNA isolated from 5 indepedent cultures (pooled after cDNA labeling). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological replicate, frozen aliquots (500μl) of E. coli K12 stock cultures were subcultured in 10 ml of Brain Heart Infusion (BHI) and incubated overnight at 37°C. Cells were then sub-cultured (1% v PGCGROWTHCONDITIONS
Frozen cell pellets were lyzed with lysozyme (Sigma Aldrich) and proteinase K (Qiagen Inc.) at room temperature. Total RNA was isolated from cell lysates using RNeasy Midi Kit according to the manufacturer's instructions (Qiagen Inc.). All RNA samples were then treated with DNase I (Ambion, Life technologies) before a phenol PGCGROWTHCONDITIONS
growth phase: stationary phase (grown to an OD600nm of 0.9) PGCGROWTHCONDITIONS
growth protocol: Controls grown to an optimal temperature of 37°C PGCGROWTHCONDITIONS
growth protocol: Treatment 1 (58°C F = 2) PGCGROWTHCONDITIONS
growth protocol: Treatment 2 (58°C F = 3) PGCGROWTHCONDITIONS
growth protocol: Treatment 3 (60°C F = 3) PGCGROWTHCONDITIONS
growth protocol: Treatment 4 (core temperature of 71°C) PGCGROWTHCONDITIONS
LOWESS normalized data obtained from log2 of processed Red signal (treated) PGCGROWTHCONDITIONS
strain: strain K12 substrain MG1655 PGCGROWTHCONDITIONS
Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 40min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 80min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, prior to CORM-3 addition PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 40min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 80min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, prior to CORM-3 addition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 10_Anaerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 11_Anaerobic culture_CORM-3_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 12_Anaerobic culture_CORM-3_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 18_Aerobic culture_CORM-3_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 19_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 20_Aerobic culture_CORM-3_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 25_Aerobic culture_iCORM-3_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 26_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 28_Anaerobic culture_iCORM-3_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 29_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 30_Anaerobic culture_iCORM-3_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
strain: Wild type strain MG1655 PGCGROWTHCONDITIONS
Total RNA extracted using Trizol following manufacturer's instructions PGCGROWTHCONDITIONS
dpiA 2x Overexpression pHI1429 in LB at 37 Mid Log Phase PGCGROWTHCONDITIONS
dpiAoverexpressor PGCGROWTHCONDITIONS
ecd3-c-0081429 wt vs dpiAoverexpressor PGCGROWTHCONDITIONS
ecd3-c-0101429 wt vs dpiAoverexpressor PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) PGCGROWTHCONDITIONS
WT1088 in LB at 37 Mid Log Phase PGCGROWTHCONDITIONS
WT1088 vs. dpiA 2x Overexpression pHI1429 in LB at 37 Mid Log Phase Trial A PGCGROWTHCONDITIONS
WT1088 vs. dpiA 2x Overexpression pHI1429 in LB at 37 Mid Log Phase Trial B PGCGROWTHCONDITIONS
antibody: Affinity Purified FNR antibody PGCGROWTHCONDITIONS
antibody: Pre-cleared FNR antibody PGCGROWTHCONDITIONS
antibody: Pre-cleared H-NS polyclonal antibody PGCGROWTHCONDITIONS
antibody: Pre-cleared IHF polyclonal antibody PGCGROWTHCONDITIONS
antibody: RNA Polymerase ß monoclonal antibody from NeoClone (W0002) PGCGROWTHCONDITIONS
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown aerobically (25% O2, 70% N2 and 5% CO2) until mid-log phase (OD600 of 0.35) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Cells were grown with 16 µM IPTG and 300 µL Cm20 anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Cells were grown with 4 µM IPTG and 300 µL Cm20 anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Cells were grown with 8 µM IPTG and 300 µL Cm20 anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655star PGCGROWTHCONDITIONS
FNR - Anaerobic - A PGCGROWTHCONDITIONS
FNR - Anaerobic - Affinity Purified - A PGCGROWTHCONDITIONS
FNR - Anaerobic - Affinity Purified - B PGCGROWTHCONDITIONS
FNR - Anaerobic - B PGCGROWTHCONDITIONS
FNR - Anaerobic - C PGCGROWTHCONDITIONS
∆fnr - Anaeroibc PGCGROWTHCONDITIONS
FNR ChIP DNA from ∆hns PGCGROWTHCONDITIONS
∆fnr ChIP DNA from PK4854 PGCGROWTHCONDITIONS
FNR ChIP DNA from WT Escherchia coli MG1655 K-12 PGCGROWTHCONDITIONS
FNR - ∆hns∆stpA A PGCGROWTHCONDITIONS
FNR - ∆hns∆stpA B PGCGROWTHCONDITIONS
FNR INPUT from PK8263 with 16 µM INPUTTG PGCGROWTHCONDITIONS
FNR INPUT from PK8263 with 4 µM INPUTTG PGCGROWTHCONDITIONS
FNR INPUT from PK8263 with 8 µM INPUTTG PGCGROWTHCONDITIONS
FNR INPUT from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
FNR IP from PK8263 with 16 µM IPTG PGCGROWTHCONDITIONS
FNR IP from PK8263 with 4 µM IPTG PGCGROWTHCONDITIONS
FNR IP from PK8263 with 8 µM IPTG PGCGROWTHCONDITIONS
FNR IP from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
growth condition: 16 µM IPTG PGCGROWTHCONDITIONS
growth condition: 4 µM IPTG PGCGROWTHCONDITIONS
growth condition: 8 µM IPTG PGCGROWTHCONDITIONS
growth condition: Aerobic PGCGROWTHCONDITIONS
growth condition: anaerobic PGCGROWTHCONDITIONS
growth condition: Anaerobic PGCGROWTHCONDITIONS
HNS - Aerobic A PGCGROWTHCONDITIONS
HNS - Aerobic B PGCGROWTHCONDITIONS
HNS - Anaerobic A PGCGROWTHCONDITIONS
HNS - Anaerobic B PGCGROWTHCONDITIONS
HNS ChIP DNA from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
HNS ChIP DNA from WT Escherichia coli MG1655 K-12 Replicate B PGCGROWTHCONDITIONS
IHF - Anaerobic A PGCGROWTHCONDITIONS
IHF - Anaerobic B PGCGROWTHCONDITIONS
IHF ChIP DNA from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
IHF ChIP DNA from WT Escherichia coli MG1655 K-12 Replicate B PGCGROWTHCONDITIONS
INPUT ChIP DNA from ∆hns PGCGROWTHCONDITIONS
INPUT ChIP DNA from WT Escherchia coli MG1655 K-12, no antibody control PGCGROWTHCONDITIONS
INPUT ChIP DNA from WT Escherchia coli MG1655 K-12, no antibody control, Replicate B PGCGROWTHCONDITIONS
INPUT ChIP DNA from WTPK4854, no antibody control PGCGROWTHCONDITIONS
Ptac::fnr - A - 16 µM IPTG PGCGROWTHCONDITIONS
Ptac::fnr - A - 4 µM IPTG PGCGROWTHCONDITIONS
Ptac::fnr - A - 8 µM IPTG PGCGROWTHCONDITIONS
Ptac::fnr - B - 16 µM IPTG PGCGROWTHCONDITIONS
Ptac::fnr - B - 4 µM IPTG PGCGROWTHCONDITIONS
Ptac::fnr - B - 8 µM IPTG PGCGROWTHCONDITIONS
Ptac::fnr - C - 16 µM IPTG PGCGROWTHCONDITIONS
ß - Aerobic - A PGCGROWTHCONDITIONS
ß - Aerobic - B PGCGROWTHCONDITIONS
ß - Anaerobic - A PGCGROWTHCONDITIONS
ß - Anaerobic - B PGCGROWTHCONDITIONS
ß ChIP DNA from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
strain: ∆hns PGCGROWTHCONDITIONS
strain: MG1655 K-12 WT PGCGROWTHCONDITIONS
strain: PK4854 PGCGROWTHCONDITIONS
strain: PK8263 PGCGROWTHCONDITIONS
tag: MG1655 K-12 WT PGCGROWTHCONDITIONS
10 ng of DNA were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting either 275 bp fragments (s70 libraries) or 400 bp fragments (FNR libraries).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx.  A paired read, 100 bp runs were used for one replicate of each s70 aerobic and anaerobic growth conditions, using standard SBS kits (v4) and SCS 2.6 on an Illumina HiSeq.  Basecalling was performed using the standard Illumina Pipeline version 1.6. PGCGROWTHCONDITIONS
Aerobic Cultures PGCGROWTHCONDITIONS
aerobic INPUT DNA PGCGROWTHCONDITIONS
Anaerobic Cultures PGCGROWTHCONDITIONS
anaerobic INPUT DNA PGCGROWTHCONDITIONS
Antibodies for beta of RNAP - NeoClone, Cat Number: W0002, Lot Number: 2008L10-001  Antibodies for sigma70 of RNAP - NeoClone, Cat Number: W0004, Lot Number: 2008K12-001  All other antibodies (FNR, H-NS, IHF) were produced in this study and are not commercially available. PGCGROWTHCONDITIONS
antibody: Affinity purified FNR polyclonal antibody PGCGROWTHCONDITIONS
antibody: INPUT PGCGROWTHCONDITIONS
antibody: RNA Polymerase σ70 monoclonal antibody from NeoClone (W0004) PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
DNA were submitted to the Joint Genome Institute for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting either 275 bp fragments (s70 libraries).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. Basecalling was performed using the standard Illumina Pipeline version 1.6. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655star PGCGROWTHCONDITIONS
FNR IP ChIP-seq Anaerobic A PGCGROWTHCONDITIONS
FNR_IP_ChIP-seq_Anaerobic_A_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
FNR IP ChIP-seq Anaerobic B PGCGROWTHCONDITIONS
FNR_IP_ChIP-seq_Anaerobic_B_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
growth condition: Aerobic Cultures PGCGROWTHCONDITIONS
growth condition: Anaerobic Cultures PGCGROWTHCONDITIONS
INPUT_ChIP-seq_Aerobic_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
INPUT_ChIP-seq_Anaerobic_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
INPUT DNA B PGCGROWTHCONDITIONS
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads. PGCGROWTHCONDITIONS
Sigma70_IP_ChIP-seq_Aerobic_A_SET_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
Sigma70_IP_ChIP-seq_Anaerobic_A_SET_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
strain: Wild Type K-12 PGCGROWTHCONDITIONS
σ70 IP ChIP-seq Aerobic A PGCGROWTHCONDITIONS
σ70 IP ChIP-seq Aerobic B PGCGROWTHCONDITIONS
σ70 IP ChIP-seq Anaerobic A PGCGROWTHCONDITIONS
σ70 IP ChIP-seq Anaerobic B PGCGROWTHCONDITIONS
Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (ref). Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop. To enrich for mRNA, the 23S and 16S rRNA were removed using the Ambion MICROBExpress kit (Ambion) following manufacturer’s guidelines, except the total RNA was incubated with the rRNA oligonucleotides for one hour instead of 15 minutes. PGCGROWTHCONDITIONS
Ecoli_dFNR_rep1_anaerobic PGCGROWTHCONDITIONS
Ecoli_dFNR_rep2_anaerobic PGCGROWTHCONDITIONS
Ecoli_wild-type_rep1_anaerobic PGCGROWTHCONDITIONS
Ecoli_wild-type_rep2_anaerobic PGCGROWTHCONDITIONS
Escherichia coli MG1655 K-12 dFNR (PK4854) PGCGROWTHCONDITIONS
Escherichia coli MG1655 K-12 WT PGCGROWTHCONDITIONS
Escherichia coli MG1655 K-12 WT and ∆fnr were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Ref). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655star PGCGROWTHCONDITIONS
FNR-_Anaerobic_RNAseq_A_Tag_Count.txt: U00096.2 PGCGROWTHCONDITIONS
FNR-_Anaerobic_RNAseq_A_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
FNR-_Anaerobic_RNAseq_B_Tag_Count.txt: U00096.2 PGCGROWTHCONDITIONS
FNR-_Anaerobic_RNAseq_B_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
genoype: dFNR PGCGROWTHCONDITIONS
genoype: Wild-Type PGCGROWTHCONDITIONS
growth condition: anaerobic PGCGROWTHCONDITIONS
phenotype: lacking FNR protein PGCGROWTHCONDITIONS
phenotype: normal PGCGROWTHCONDITIONS
Resulting reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle & Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
The RNAs were chemically fragmented using RNA Fragmentation Reagents (Ambion) to the size range of 200-250 bp using 1x fragmentation solution for 5 minutes at 70°C (Ambion).  Double stranded cDNA was generated using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) following the manufacturer’s protocol.  The Illumina Paired End Sample Prep kit was used for Illumina RNA-seq library creation using the manufacturer’s instructions.  Briefly, the fragmented cDNA was end repaired, ligated to Illumina specific adapters and amplified with 10 cycles of PCR using the TruSeq SR Cluster Kit (v2).  Single-end 36 bp reads were generated by sequencing on the Illumina Genome Analyzer IIx, using the TruSeq SBS Kit (v5) following the manufacturer’s protocol. PGCGROWTHCONDITIONS
WT_Anaerobic_RNAseq_A_Tag_Count.txt: U00096.2 PGCGROWTHCONDITIONS
WT_Anaerobic_RNAseq_A_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
WT_Anaerobic_RNAseq_B_Tag_Count.txt: U00096.2 PGCGROWTHCONDITIONS
WT_Anaerobic_RNAseq_B_WIG.wig: U00096.2 PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final). PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
cell type: bacterial cells PGCGROWTHCONDITIONS
chip antibody: anti-b(RNAP) NT63 PGCGROWTHCONDITIONS
chip antibody: anti-H-NS PGCGROWTHCONDITIONS
chip antibody cat. #: W0002 PGCGROWTHCONDITIONS
chip antibody vendor: Neoclone PGCGROWTHCONDITIONS
Datasets were normalized using locally weighted linear regression (LOWESS) normalization on raw Cy3 and Cy5 signals to correct for intensity-dependent dye effects within each array using the “normalizeWithinArrays” function in the limma package for the statistical program R (v.2.14.2). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
H-NS ChIP DNA from MG1655 cells PGCGROWTHCONDITIONS
Input DNA from MDS42 cells PGCGROWTHCONDITIONS
Input DNA from MDS42 ΔnusA* cells PGCGROWTHCONDITIONS
Input DNA from MDS42 ΔnusG cells PGCGROWTHCONDITIONS
Input DNA from MG1655 cells PGCGROWTHCONDITIONS
Input DNA from MG1655 Δhns cells PGCGROWTHCONDITIONS
MDS42 RNAP 1 PGCGROWTHCONDITIONS
MDS42 RNAP 2 PGCGROWTHCONDITIONS
MDS42 ΔnusA* RNAP 1 PGCGROWTHCONDITIONS
MDS42 ΔnusA* RNAP 2 PGCGROWTHCONDITIONS
MDS42 ΔnusG RNAP 1 PGCGROWTHCONDITIONS
MDS42 ΔnusG RNAP 2 PGCGROWTHCONDITIONS
MG1655 H-NS 1 PGCGROWTHCONDITIONS
MG1655 H-NS 2 PGCGROWTHCONDITIONS
MG1655 RNAP 1 PGCGROWTHCONDITIONS
MG1655 RNAP 2 PGCGROWTHCONDITIONS
MG1655 Δhns RNAP 1 PGCGROWTHCONDITIONS
MG1655 Δhns RNAP 2 PGCGROWTHCONDITIONS
RNAP ChIP DNA from MDS42 cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from MDS42 ΔnusA* cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from MDS42 ΔnusG cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from MG1655 cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from MG1655 Δhns cells PGCGROWTHCONDITIONS
sample type: input DNA PGCGROWTHCONDITIONS
strain: MDS42 (RL1961) PGCGROWTHCONDITIONS
strain: MG1655 (RL1655) PGCGROWTHCONDITIONS
strain: RL2673 PGCGROWTHCONDITIONS
strain: RSW421 (RL1962) PGCGROWTHCONDITIONS
strain: RSW422 (RL1963) PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
Cultures were transferred directly into an ice-cold ethanol PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
MDS42 PGCGROWTHCONDITIONS
MDS42 1 PGCGROWTHCONDITIONS
MDS42 2 PGCGROWTHCONDITIONS
MDS42 + 20 ug PGCGROWTHCONDITIONS
MDS42 ΔnusA* PGCGROWTHCONDITIONS
MDS42 ΔnusA* 1 PGCGROWTHCONDITIONS
MDS42 ΔnusA* 2 PGCGROWTHCONDITIONS
MDS42 ΔnusG PGCGROWTHCONDITIONS
MDS42 ΔnusG 1 PGCGROWTHCONDITIONS
MDS42 ΔnusG 2 PGCGROWTHCONDITIONS
Raw probe intensities were normalized across samples using RMA analysis implemented in the NimbleScan software package (v.2.4). PGCGROWTHCONDITIONS
strain: MDS42 (RL1961) PGCGROWTHCONDITIONS
strain: RSW421 (RL1962) PGCGROWTHCONDITIONS
strain: RSW421 (RL1967) PGCGROWTHCONDITIONS
strain: RSW422 (RL1963) PGCGROWTHCONDITIONS
strain: RSW472 (RL1966) PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. PGCGROWTHCONDITIONS
treated with: 20 ug PGCGROWTHCONDITIONS
Δrac PGCGROWTHCONDITIONS
Δrac 1 PGCGROWTHCONDITIONS
Δrac 2 PGCGROWTHCONDITIONS
Δrac + 20 ug PGCGROWTHCONDITIONS
Δrac ΔnusG PGCGROWTHCONDITIONS
Δrac ΔnusG 1 PGCGROWTHCONDITIONS
Δrac ΔnusG 2 PGCGROWTHCONDITIONS
Base calling was performed by the DOE Joint Genome Institute using Illumina software. PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
Counts per million unique reads were calculated for each gene. PGCGROWTHCONDITIONS
Cultures were transferred directly into an ice-cold ethanol PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
MG1655 1 PGCGROWTHCONDITIONS
MG1655 2 PGCGROWTHCONDITIONS
MG1655 + 20 ug PGCGROWTHCONDITIONS
molecule subtype: ribosome-depeleted RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85 PGCGROWTHCONDITIONS
Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents. PGCGROWTHCONDITIONS
1 ml of VWPE extract (1 mg PGCGROWTHCONDITIONS
agent: control (1 ml of LB broth added) PGCGROWTHCONDITIONS
agent: ethanol (1 ml of ethanol 20% added) PGCGROWTHCONDITIONS
agent: polyphenols (1 ml of OVWPE diluted in ethanol 20% added) PGCGROWTHCONDITIONS
Data processed with FeatureExtraction v9.5.1 and quantile normalized using R2.6.1 statistical software PGCGROWTHCONDITIONS
E.coli, control culture, 20 minutes (t2) after treatment, replicate A PGCGROWTHCONDITIONS
E.coli, control culture, 20 minutes (t2) after treatment, replicate B PGCGROWTHCONDITIONS
E.coli, control culture, 20 minutes (t2) after treatment, replicate C PGCGROWTHCONDITIONS
E.coli, control culture, 40 minutes (t3) after treatment, replicate A PGCGROWTHCONDITIONS
E.coli, control culture, 40 minutes (t3) after treatment, replicate B PGCGROWTHCONDITIONS
E.coli, control culture, 40 minutes (t3) after treatment, replicate C PGCGROWTHCONDITIONS
E.coli, control culture, at the time of treatment (t1), replicate A PGCGROWTHCONDITIONS
E.coli, control culture, at the time of treatment (t1), replicate B PGCGROWTHCONDITIONS
E.coli, control culture, at the time of treatment (t1), replicate C PGCGROWTHCONDITIONS
E.coli_control_repA_t1 PGCGROWTHCONDITIONS
E.coli_control_repA_t2 PGCGROWTHCONDITIONS
E.coli_control_repA_t3 PGCGROWTHCONDITIONS
E.coli_control_repB_t1 PGCGROWTHCONDITIONS
E.coli_control_repB_t2 PGCGROWTHCONDITIONS
E.coli_control_repB_t3 PGCGROWTHCONDITIONS
E.coli_control_repC_t1 PGCGROWTHCONDITIONS
E.coli_control_repC_t2 PGCGROWTHCONDITIONS
E.coli_control_repC_t3 PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, 20 minutes (t2) after treatment, replicate A PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, 20 minutes (t2) after treatment, replicate B PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, 20 minutes (t2) after treatment, replicate C PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, 40 minutes (t3) after treatment, replicate A PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, 40 minutes (t3) after treatment, replicate B PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, 40 minutes (t3) after treatment, replicate C PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, at the time of treatment (t1), replicate A PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, at the time of treatment (t1), replicate B PGCGROWTHCONDITIONS
E.coli, culture with ethanol 20%, at the time of treatment (t1), replicate C PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, 20 minutes (t2) after treatment, replicate A PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, 20 minutes (t2) after treatment, replicate B PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, 20 minutes (t2) after treatment, replicate C PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, 40 minutes (t3) after treatment, replicate A PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, 40 minutes (t3) after treatment, replicate B PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, 40 minutes (t3) after treatment, replicate C PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, at the time of treatment (t1), replicate A PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, at the time of treatment (t1), replicate B PGCGROWTHCONDITIONS
E.coli, culture with VWPE extract diluted in ethanol 20%, at the time of treatment (t1), replicate C PGCGROWTHCONDITIONS
E.coli_ethanol_repA_t1 PGCGROWTHCONDITIONS
E.coli_ethanol_repA_t2 PGCGROWTHCONDITIONS
E.coli_ethanol_repA_t3 PGCGROWTHCONDITIONS
E.coli_ethanol_repB_t1 PGCGROWTHCONDITIONS
E.coli_ethanol_repB_t2 PGCGROWTHCONDITIONS
E.coli_ethanol_repB_t3 PGCGROWTHCONDITIONS
E.coli_ethanol_repC_t1 PGCGROWTHCONDITIONS
E.coli_ethanol_repC_t2 PGCGROWTHCONDITIONS
E.coli_ethanol_repC_t3 PGCGROWTHCONDITIONS
E.coli K12 was cultured in LB and grown at 37°C PGCGROWTHCONDITIONS
E.coli_polyphenols_repA_t1 PGCGROWTHCONDITIONS
E.coli_polyphenols_repA_t2 PGCGROWTHCONDITIONS
E.coli_polyphenols_repA_t3 PGCGROWTHCONDITIONS
E.coli_polyphenols_repB_t1 PGCGROWTHCONDITIONS
E.coli_polyphenols_repB_t2 PGCGROWTHCONDITIONS
E.coli_polyphenols_repB_t3 PGCGROWTHCONDITIONS
E.coli_polyphenols_repC_t1 PGCGROWTHCONDITIONS
E.coli_polyphenols_repC_t2 PGCGROWTHCONDITIONS
E.coli_polyphenols_repC_t3 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
RNA extracted according to QiAgen RNeasy MiniKit protocol for bacterial samples PGCGROWTHCONDITIONS
time: 20 minutes (t2) after treatment PGCGROWTHCONDITIONS
time: 40 minutes (t3) after treatment PGCGROWTHCONDITIONS
time: at time of treatment (t1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
genotype: yajL mutant PGCGROWTHCONDITIONS
growth phase: exponential PGCGROWTHCONDITIONS
Intensity measures in wild type strain, replicate 1 PGCGROWTHCONDITIONS
Intensity measures in wild type strain, replicate 2 PGCGROWTHCONDITIONS
Intensity measures in yajL mutant strain, replicate 1 PGCGROWTHCONDITIONS
Intensity measures in yajL mutant strain, replicate 2 PGCGROWTHCONDITIONS
Luria broth (LB) medium under aeration, exponential phase OD600 = 0.3. PGCGROWTHCONDITIONS
RNA extraction was performed using phenol treatment. PGCGROWTHCONDITIONS
strain PGCGROWTHCONDITIONS
The CEL files generated for each array were analyzed using Affymetrix Expression Console software. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
Untreated wild type versus untreated yajL mutant. PGCGROWTHCONDITIONS
wild type MG1655 PGCGROWTHCONDITIONS
yajL mutant (genetic background MG1655) PGCGROWTHCONDITIONS
At OD600 of 0.5, cell cultures were separated into two flasks. D-galactose (final 0.3%) was added to one and cells were grown for 1.5 h further. PGCGROWTHCONDITIONS
Cells were then placed on ice and RNAprotect™ bacteria reagent (Qiagen) was added to stabilize the RNA. Total RNAs of cells were purified by RNeasy mini kit (Qiagen). Isolated RNA (10 ug) was used for random primer cDNA synthesis using SuperScript II reverse transcriptase, 18064–071 (Invitrogen). The reaction mixture was then subsequently treated with 1 N NaOH to degrade any remaining RNA and treated with 1 N HCl to neutralize the NaOH. Synthesized cDNA was then purified using MiniElute PCR purification columns, 28004 (Qiagen). Purified cDNA (3 ug) was fragmented to between 50 and 200 bps by 0.6 U PGCGROWTHCONDITIONS
Computation of genomic intervals based on computed signal and p-values PGCGROWTHCONDITIONS
Computation of summary statistics PGCGROWTHCONDITIONS
E. coli galT mutant cells were cultivated in 125-mL corning flasks containing 30 mL of M63 minimal medium plus glycerol (final 0.3%) at 37 °C. PGCGROWTHCONDITIONS
E. coli galT mutant with galactose PGCGROWTHCONDITIONS
E. coli galT mutant without galactose PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Signal and p-values for each genomic position interrogated. PGCGROWTHCONDITIONS
The program used to generate the bed PGCGROWTHCONDITIONS
The TAS software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces: PGCGROWTHCONDITIONS
Visualizations for assessing the quality of the array data PGCGROWTHCONDITIONS
with D-galactose PGCGROWTHCONDITIONS
without D-galactose PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 0 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 10 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 2.5 min after induction PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 5 min after induction PGCGROWTHCONDITIONS
Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA). PGCGROWTHCONDITIONS
Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot PGCGROWTHCONDITIONS
EC18n122 RpoH 10 min Time course 4 PGCGROWTHCONDITIONS
EC18n167 RpoH 0 min Time course 2 PGCGROWTHCONDITIONS
EC18n168 RpoH 2.5 min Time course 2 PGCGROWTHCONDITIONS
EC18n169 RpoH 5 min Time course 2 PGCGROWTHCONDITIONS
EC18n170 RpoH 10 min Time course 2 PGCGROWTHCONDITIONS
EC18n171 RpoH 20 min Time course 2 PGCGROWTHCONDITIONS
EC18n177 RpoH 0 min Time course 1 PGCGROWTHCONDITIONS
EC18n178 RpoH 2.5 min Time course 1 PGCGROWTHCONDITIONS
EC18n179 RpoH 5 min Time course 1 PGCGROWTHCONDITIONS
EC18n180 RpoH 10 min Time course 1 PGCGROWTHCONDITIONS
EC18n181 RpoH 20 min Time course 1 PGCGROWTHCONDITIONS
EC18n182 RpoH 0 min Time course 3 PGCGROWTHCONDITIONS
EC18n183 RpoH 2.5 min Time course 3 PGCGROWTHCONDITIONS
EC18n184 RpoH 5 min Time course 3 PGCGROWTHCONDITIONS
EC18n185 RpoH 10 min Time course 3 PGCGROWTHCONDITIONS
EC18n186 RpoH 20 min Time course 3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm PGCGROWTHCONDITIONS
MG1655 PhtpG::lacZ delta lacX74 PGCGROWTHCONDITIONS
RpoH induced (0 min) PGCGROWTHCONDITIONS
RpoH induced (10 min) PGCGROWTHCONDITIONS
RpoH induced (20 min) PGCGROWTHCONDITIONS
RpoH induced (2.5 min) PGCGROWTHCONDITIONS
RpoH induced (5 min) PGCGROWTHCONDITIONS
Wild type control (0 min) PGCGROWTHCONDITIONS
Wild type control (10 min) PGCGROWTHCONDITIONS
Wild type control (20 min) PGCGROWTHCONDITIONS
Wild type control (2.5 min) PGCGROWTHCONDITIONS
Wild type control (5 min) PGCGROWTHCONDITIONS
Ecoli_Ampicillin treatment T1 PGCGROWTHCONDITIONS
Ecoli_Ampicillin treatment T2 PGCGROWTHCONDITIONS
Ecoli_Ampicillin treatment T3 PGCGROWTHCONDITIONS
Ecoli_Ampicillin treatment T4 PGCGROWTHCONDITIONS
Ecoli_Ampicillin treatment T5 PGCGROWTHCONDITIONS
Ecoli_Ampicillin treatment T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 10 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 20 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 40 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 50 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 5 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min after Ampicillin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, M9 + glucose, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_CaCl2 wash T1 PGCGROWTHCONDITIONS
Ecoli_CaCl2 wash T2 PGCGROWTHCONDITIONS
Ecoli_CaCl2 wash T3 PGCGROWTHCONDITIONS
Ecoli_CaCl2 wash T4 PGCGROWTHCONDITIONS
Ecoli_CaCl2 wash T5 PGCGROWTHCONDITIONS
Ecoli_CaCl2 wash T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.43 LB PGCGROWTHCONDITIONS
Escherichia coli MG1655,Sample washed in 0.1 M CaCl2 + 15 % glycerol vs before washing OD 0.43 in LB, 10 min timepoint PGCGROWTHCONDITIONS
Escherichia coli MG1655,Sample washed in 0.1 M CaCl2 + 15 % glycerol vs before washing OD 0.43 in LB, 20 min timepoint PGCGROWTHCONDITIONS
Escherichia coli MG1655,Sample washed in 0.1 M CaCl2 + 15 % glycerol vs before washing OD 0.43 in LB, 2 min timepoint PGCGROWTHCONDITIONS
Escherichia coli MG1655,Sample washed in 0.1 M CaCl2 + 15 % glycerol vs before washing OD 0.43 in LB, 40 min timepoint PGCGROWTHCONDITIONS
Escherichia coli MG1655,Sample washed in 0.1 M CaCl2 + 15 % glycerol vs before washing OD 0.43 in LB, 5 min timepoint PGCGROWTHCONDITIONS
Escherichia coli MG1655,Sample washed in 0.1 M CaCl2 + 15 % glycerol vs before washing OD 0.43 in LB, 60 min timepoint PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T1 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T2 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T3 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T4 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T5 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T6 PGCGROWTHCONDITIONS
Ecoli_Early Recovery in LB T7 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 90 min recovery in LB + glucose at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel OD~0.5 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Indol-acrylate (10 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min after Indol-acrylate (10 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min after Indol-acrylate (10 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 5 min after Indol-acrylate (10 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min after Indol-acrylate (10 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Indol-acrylate (15 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min after Indol-acrylate (15 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min after Indol-acrylate (15 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 5 min after Indol-acrylate (15 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min after Indol-acrylate (15 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Kanamycin treatment T1 PGCGROWTHCONDITIONS
Ecoli_Kanamycin treatment T2 PGCGROWTHCONDITIONS
Ecoli_Kanamycin treatment T3 PGCGROWTHCONDITIONS
Ecoli_Kanamycin treatment T4 PGCGROWTHCONDITIONS
Ecoli_Kanamycin treatment T5 PGCGROWTHCONDITIONS
Ecoli_Kanamycin treatment T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 10 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 20 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 40 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 50 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 5 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min after Kanamycin (100 ug PGCGROWTHCONDITIONS
Escherichia coli MG1655, M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, M9 + glucose, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_LB growth T1 PGCGROWTHCONDITIONS
Ecoli_LB growth T10 PGCGROWTHCONDITIONS
Ecoli_LB growth T11 PGCGROWTHCONDITIONS
Ecoli_LB growth T2 PGCGROWTHCONDITIONS
Ecoli_LB growth T3 PGCGROWTHCONDITIONS
Ecoli_LB growth T4 PGCGROWTHCONDITIONS
Ecoli_LB growth T5 PGCGROWTHCONDITIONS
Ecoli_LB growth T6 PGCGROWTHCONDITIONS
Ecoli_LB growth T7 PGCGROWTHCONDITIONS
Ecoli_LB growth T8 PGCGROWTHCONDITIONS
Ecoli_LB growth T9 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 105 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 133 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 1440 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 163 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 191 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 218 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 261 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 313 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 443 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, 78 min recovery in LB+0.2% glc PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel OD~0.5 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T1 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T2 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T3 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T4 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T5 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T6 PGCGROWTHCONDITIONS
Ecoli_Late Recovery in LB T7 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 90 min recovery in LB + glucose at OD 1.0 PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel OD~0.5 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_NOX+_balanced growth at OD 0.13 PGCGROWTHCONDITIONS
Ecoli_NOX+_balanced growth at OD 0.21 PGCGROWTHCONDITIONS
Ecoli_NOX+_balanced growth at OD 0.28 PGCGROWTHCONDITIONS
Ecoli_NOX+_balanced growth at OD 0.34 PGCGROWTHCONDITIONS
Ecoli_NOX+_balanced growth at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_NOX-_balanced groNOX-h at OD 0.19 PGCGROWTHCONDITIONS
Ecoli_NOX-_balanced groNOX-h at OD 0.3 PGCGROWTHCONDITIONS
Ecoli_NOX-_balanced groNOX-h at OD 0.41 PGCGROWTHCONDITIONS
Ecoli_NOX-_balanced groNOX-h at OD 0.49 PGCGROWTHCONDITIONS
Ecoli_NOX-_balanced groNOX-h at OD 0.6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli C600 , 10 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 , 20min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 , 2 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 , 30 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 , 5 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 , LB PGCGROWTHCONDITIONS
Escherichia coli C600 , LB, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_gyrArparCr_Norfloxacin (15 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 10 min after Norfloxacin (15 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 20min after Norfloxacin (15 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 2 min after Norfloxacin (15 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 30 min after Norfloxacin (15 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 5 min after Norfloxacin (15 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), LB PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), LB, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_gyrArparCr_Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 10 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 20min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 2 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 30 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), 5 min after Norfloxacin (50 ug PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), LB PGCGROWTHCONDITIONS
Escherichia coli C600 (gyrArparCr), LB, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T1 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T2 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T3 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T4 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T5 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T6 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P T7 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, 90 min recovery in 10mM Na-P PGCGROWTHCONDITIONS
Escherichia coli MG1655, 90 min recovery in 10 mM Na-P (pH 7.5) PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel OD~0.5 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T1 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T2 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T3 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T4 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T5 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T6 PGCGROWTHCONDITIONS
Ecoli_Recovery in 10mM Na-P + 0.2 % glucose T7 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 15 min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 30 min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 45min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 75 min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, 90 min recovery in 10mM Na-P + 0.2 % glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, 90 min recovery in 10 mM Na-P + 0.2 % glucose (pH 7.5) at OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, Bonner-Vogel OD~0.5 PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Sodium Azide treatment T1 PGCGROWTHCONDITIONS
Ecoli_Sodium Azide treatment T2 PGCGROWTHCONDITIONS
Ecoli_Sodium Azide treatment T3 PGCGROWTHCONDITIONS
Ecoli_Sodium Azide treatment T4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli W3110, 0  min before treatment, Bonner-Vogel + 50 ug PGCGROWTHCONDITIONS
Escherichia coli W3110, 0 min before treatment in Bonner-Vogel + 50 ug PGCGROWTHCONDITIONS
Escherichia coli W3110,5 min 0.01 M Sodium Azide treatment vs 0 min before treatment in Bonner-Vogel + 50 ug PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T1 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T2 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T3 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T4 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose, reference Genomic DNA T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 genomic DNA PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.03, anaerobic growth in M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.2, anaerobic growth in M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 0.35, anaerobic growth in M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.6, anaerobic growth in M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 0.9, anaerobic growth in M9 + glucose PGCGROWTHCONDITIONS
Escherichia coli MG1655,  stationary phase anaerobic growth in M9 + glucose PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T1 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T2 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T3 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T4 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate,reference Genomic DNA T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 genomic DNA PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.05, anaerobic growth in M9 + glucose + fumarate, PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.21, anaerobic growth in M9 + glucose + fumarate, PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 0.43, anaerobic growth in M9 + glucose + fumarate, PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.7, anaerobic growth in M9 + glucose + fumarate, PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 1.2, anaerobic growth in M9 + glucose + fumarate, PGCGROWTHCONDITIONS
Escherichia coli MG1655,  stationary phase anaerobic growth in M9 + glucose + fumarate, PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T1 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T2 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T3 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T4 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose vs Aerobic OD 0.4 T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli MG1655 Aerobic growth OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655 Aerobic growth on M9 +glucose, OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.08, anaerobic growth in M9 + glucose , PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.15, anaerobic growth in M9 + glucose , PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 0.34, anaerobic growth in M9 + glucose , PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.73, anaerobic growth in M9 + glucose , PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 1.02, anaerobic growth in M9 + glucose , PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 1.27 anaerobic growth in M9 + glucose , PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T1 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T2 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T3 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T4 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T5 PGCGROWTHCONDITIONS
Ecoli_Anaerobic growth in M9 + glucose + fumarate vs Aerobic OD 0.4 T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli MG1655 Aerobic growth on M9 + glucose + fumarate,OD 0.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.15, anaerobic growth in M9 + glucose + fumarate , PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.30, anaerobic growth in M9 + glucose + fumarate , PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 0.63, anaerobic growth in M9 + glucose + fumarate , PGCGROWTHCONDITIONS
Escherichia coli MG1655, OD 0.85, anaerobic growth in M9 + glucose + fumarate , PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 1.07, anaerobic growth in M9 + glucose + fumarate , PGCGROWTHCONDITIONS
Escherichia coli MG1655,  OD 1.29 anaerobic growth in M9 + glucose + fumarate , PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Gamma treatment T1 PGCGROWTHCONDITIONS
Ecoli_Gamma treatment T2 PGCGROWTHCONDITIONS
Ecoli_Gamma treatment T3 PGCGROWTHCONDITIONS
Ecoli_Gamma treatment T4 PGCGROWTHCONDITIONS
Ecoli_Gamma treatment T5 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655, 0 min before treatment, Davis PGCGROWTHCONDITIONS
Escherichia coli MG1655, 10 min after Gamma treatment in Davis PGCGROWTHCONDITIONS
Escherichia coli MG1655, 20 min after Gamma treatment in Davis PGCGROWTHCONDITIONS
Escherichia coli MG1655, 40min after Gamma treatment in Davis PGCGROWTHCONDITIONS
Escherichia coli MG1655, 5 min after Gamma treatment in Davis PGCGROWTHCONDITIONS
Escherichia coli MG1655, 60 min after Gamma treatment in Davis PGCGROWTHCONDITIONS
Escherichia coli MG1655, Davis, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Novobiocin treatment (200 ug PGCGROWTHCONDITIONS
Ecoli_Novobiocin treatment (20 ug PGCGROWTHCONDITIONS
Ecoli_Novobiocin treatment (50 ug PGCGROWTHCONDITIONS
Ecoli_Novobiocin treatment (5 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli LE234 acrD-, 0 min before treatment in LB PGCGROWTHCONDITIONS
Escherichia coli LE234 acrD-, 5 min after Novobiocin (200 ug PGCGROWTHCONDITIONS
Escherichia coli LE234 acrD-, 5 min after Novobiocin (20 ug PGCGROWTHCONDITIONS
Escherichia coli LE234 acrD-, 5 min after Novobiocin (50 ug PGCGROWTHCONDITIONS
Escherichia coli LE234 acrD-, 5 min after Novobiocin (5 ug PGCGROWTHCONDITIONS
Escherichia coli LE234 acrD-, LB, 0 min before treatment PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_pUC expression OD 0.2 PGCGROWTHCONDITIONS
Ecoli_pUC expression OD 0.5 PGCGROWTHCONDITIONS
Ecoli_pUC expression OD 0.9 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli DH5alpha (NEB), OD 0.2 in LB + Amp,  pUC expression PGCGROWTHCONDITIONS
Escherichia coli DH5alpha (NEB), OD 0.2 in LB, no pUC PGCGROWTHCONDITIONS
Escherichia coli DH5alpha (NEB), OD 0.5 in LB + Amp,  pUC expression PGCGROWTHCONDITIONS
Escherichia coli DH5alpha (NEB), OD 0.5 in LB, no pUC PGCGROWTHCONDITIONS
Escherichia coli DH5alpha (NEB), OD 0.9 in LB + Amp,  pUC expression PGCGROWTHCONDITIONS
Escherichia coli DH5alpha (NEB), OD 0.9 in LB, no pUC PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Stationary phase in LB T1 PGCGROWTHCONDITIONS
Ecoli_Stationary phase in LB T2 PGCGROWTHCONDITIONS
Ecoli_Stationary phase in LB T3 PGCGROWTHCONDITIONS
Ecoli_Stationary phase in LB T4 PGCGROWTHCONDITIONS
Ecoli_Stationary phase in LB T5 PGCGROWTHCONDITIONS
Ecoli_Stationary phase in LB T6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 genomic DNA PGCGROWTHCONDITIONS
Escherichia coli MG1655, Stationary phase in LB OD 2.4 PGCGROWTHCONDITIONS
Escherichia coli MG1655, Stationary phase in LB OD 2.8 PGCGROWTHCONDITIONS
Escherichia coli MG1655,  Stationary phase in LB OD 3.1 PGCGROWTHCONDITIONS
Escherichia coli MG1655, Stationary phase in LB OD 3.1 for 20 min PGCGROWTHCONDITIONS
Escherichia coli MG1655,  Stationary phase in LB OD 3.1 for 40 min PGCGROWTHCONDITIONS
Escherichia coli MG1655,  stationary phase in LB, OD 3.1 for 60 min PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
Ecoli_Temperature upshift in gyrBT mutant T1 PGCGROWTHCONDITIONS
Ecoli_Temperature upshift in gyrBT mutant T2 PGCGROWTHCONDITIONS
Ecoli_Temperature upshift in gyrBT mutant T3 PGCGROWTHCONDITIONS
Ecoli_Temperature upshift in gyrBT mutant T4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli W3110gyrb234, LB PGCGROWTHCONDITIONS
Escherichia coli W3110gyrb234, LB, 10 min after upshift to 42 C PGCGROWTHCONDITIONS
Escherichia coli W3110gyrb234, LB, 20 min after upshift to 42 C PGCGROWTHCONDITIONS
Escherichia coli W3110gyrb234, LB, 2 min after upshift to 42 C PGCGROWTHCONDITIONS
Escherichia coli W3110gyrb234, LB, 5 min after upshift to 42 C PGCGROWTHCONDITIONS
Normalized log (2) ratio of Cy5 PGCGROWTHCONDITIONS
CCCP-1, biological rep1 PGCGROWTHCONDITIONS
CCCP-2, biological rep2 PGCGROWTHCONDITIONS
CCCP-3, biological rep3 PGCGROWTHCONDITIONS
Control-1, biological rep1 PGCGROWTHCONDITIONS
Control-2, biological rep2 PGCGROWTHCONDITIONS
Control-3, biological rep3 PGCGROWTHCONDITIONS
E. coli_CCCP_15 min PGCGROWTHCONDITIONS
E. coli_control_30 min PGCGROWTHCONDITIONS
E. coli_gentamicin_30 min PGCGROWTHCONDITIONS
E. coli (OD660 nm = 0.3) was incubated with control protein or antibacterial preparations in 5 mM TRIS (pH 7.6) with 150 mM NaCl, 10 µM ZnSO4, and 2% LB, at 37oC aerobically with shaking. PGCGROWTHCONDITIONS
E. coli_PGRP_30 min PGCGROWTHCONDITIONS
E. coli was treated at 37C aerobically with shaking with BSA (control, 100 µg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gentamicin-1, biological rep1 PGCGROWTHCONDITIONS
Gentamicin-2, biological rep2 PGCGROWTHCONDITIONS
Gentamicin-3, biological rep3 PGCGROWTHCONDITIONS
growth phase: logarithmic growth PGCGROWTHCONDITIONS
PGRP-1, biological rep1 PGCGROWTHCONDITIONS
PGRP-2, biological rep2 PGCGROWTHCONDITIONS
PGRP-3, biological rep3 PGCGROWTHCONDITIONS
RNA was obtained from each culture using Ambion RiboPureTM-bacteria RNA extraction kit according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Signal intensities with all probes are shown in Sample data table. The 'expressed_present_probes.txt (available on Series records) contains Signal intensities with present probes.  Average signal intensities from 3 experiments were used to calculate fold increases in gene expression between treated and control groups, with signal intensity of 39 used as a minimum intensity, using the formula: average intensity in treated group PGCGROWTHCONDITIONS
strain: K-12 substrain MG1655 PGCGROWTHCONDITIONS
The hybridization intensity data signals were analyzed, normalized, and corrected for batch effect using Affymetrix GeneChip® Command Console® Software (AGCC v.3.0). Signal average, noise average, scaling factor, % present, and % absent were calculated for each probe, from which the signal intensity of >39 was calculated as reliable expression. Using this cutoff, 5531 probes were classified as present out of total 10208 probes on the array (full_expressed_data.txt). PGCGROWTHCONDITIONS
tissue: entire bacterial cell PGCGROWTHCONDITIONS
treated with: 100 µg PGCGROWTHCONDITIONS
treated with: 5 µg PGCGROWTHCONDITIONS
treated with: 800 µM CCCP for 15min PGCGROWTHCONDITIONS
BWG_butanol_3passages PGCGROWTHCONDITIONS
BWG_replicated PGCGROWTHCONDITIONS
BWY_butanol_3passages PGCGROWTHCONDITIONS
BWY_replicated PGCGROWTHCONDITIONS
Data were extracted in GenePix 4100A scanning software and normalized using the lowess method implemented in TM4 MIDAS PGCGROWTHCONDITIONS
Donor was transformed with a random genomic library made from E. coli and stored as glycerol stocks. The library was revived and transferred to four recipient strains using conjugation; the donor was miniprepped at this time, and the recipients were miniprepped after outgrowth under dual selection. Two recipient libraries in BWG and BWY were propagated under n-butanol stress for three days, and then miniprepped as well. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
Library minipreps were performed with the Zyppy Miniprep kit (Zymo Technologies) and quantified using the Qubit dsDNA BR kit (Invitrogen) and the Nanodrop spectrophotometer (Thermo Scientific) PGCGROWTHCONDITIONS
MG6_replicated PGCGROWTHCONDITIONS
MY4_replicated PGCGROWTHCONDITIONS
Plasmid DNA, after n-butanol selection PGCGROWTHCONDITIONS
Plasmid DNA, BWG post conjugation PGCGROWTHCONDITIONS
Plasmid DNA, BWY post conjugation PGCGROWTHCONDITIONS
Plasmid DNA, donor, XL1-Blue PGCGROWTHCONDITIONS
Plasmid DNA, post conjugation PGCGROWTHCONDITIONS
plasmid: Donor Library PGCGROWTHCONDITIONS
plasmid: Initial Recipient Library (BWG) PGCGROWTHCONDITIONS
plasmid: Initial Recipient Library (BWY) PGCGROWTHCONDITIONS
plasmid source: Initial Recipient Library PGCGROWTHCONDITIONS
plasmid source: Post Selection Library PGCGROWTHCONDITIONS
cell type: Persister cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
furanone-free control PGCGROWTHCONDITIONS
GeneChip Operating Software (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method, genes with a p-value of less than 0.0025 or greater than 0.9975 were considered statistically significant based on Wilcoxon signed rank test and Tukey Byweight, labeled as I and D in the attached txt file. To ensure the significance of microarray data, an additional criterion was applied to only select the genes with an expression ratio of 2 or high from this group as induced and repressed genes. PGCGROWTHCONDITIONS
RNeasy Mini Kit (Qiagen, Austin, TX, USA) with on-column DNase treatment (RNase-Free DNase Set, Qiagen). PGCGROWTHCONDITIONS
RP437 persisters treated with BF8 at 5 µg PGCGROWTHCONDITIONS
RP437 was inoculated in 100 mL LB and grown for 18 h (200 rpm, 37oC). Persister cells were isolated by lysing the normal cells with 5 µg PGCGROWTHCONDITIONS
strain: E. coli RP437 PGCGROWTHCONDITIONS
The isolated persisters were incubated in 0.85% NaCl solution for 1 h (200 rpm, 37oC) with or without 5 µg PGCGROWTHCONDITIONS
Cells of each evolved colony type were collected by centrifugation at 13,000 × g for 1 min at 4°C and were immediately used for total RNA isolation with NucleoSpin RNA II isolation kit (Macherey – Nagel, Biokè, Leiden, the Netherlands). PGCGROWTHCONDITIONS
culture type: Ancestor PGCGROWTHCONDITIONS
culture type: evolved PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Growth curves of all selected evolved colony types and the ancestor were obtained by growing them under their evolved environmental conditions in LB medium until Log-phase. For this, optical density was recorded at 600nm at a value of 0.6 to 0.7. PGCGROWTHCONDITIONS
morphology: a PGCGROWTHCONDITIONS
morphology: b PGCGROWTHCONDITIONS
morphology: c PGCGROWTHCONDITIONS
oxygen regime: daily shift between shaking and static (no shaking) conditions PGCGROWTHCONDITIONS
oxygen regime: transfers in constant static conditions PGCGROWTHCONDITIONS
oxygen regime: transfers under constant shaking (200rpm) PGCGROWTHCONDITIONS
population: 1 PGCGROWTHCONDITIONS
population: 2 PGCGROWTHCONDITIONS
population: 3 PGCGROWTHCONDITIONS
population: 4 PGCGROWTHCONDITIONS
population: 5 PGCGROWTHCONDITIONS
population: 6 PGCGROWTHCONDITIONS
population: 7 PGCGROWTHCONDITIONS
Pure culture in LB PGCGROWTHCONDITIONS
Statistical analysis was performed using R Limma package (Linear Models for Microarrays Data)  (Smyth 2004), where the two microarrays per sample were normalized using lowess normalization method. Multiple-gene probes results were merged and normalized using the MA table conversion tool available on the MOLGEN Bioinformatics Server (http: PGCGROWTHCONDITIONS
strain: MC1000 PGCGROWTHCONDITIONS
Treatment A Population 1 Colony a replica 1 PGCGROWTHCONDITIONS
Treatment A Population 1 Colony a replica 2 PGCGROWTHCONDITIONS
Treatment A Population 1 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment A Population 1 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment A Population 1 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment A Population 1 Colony c replica 2 PGCGROWTHCONDITIONS
Treatment A Population 2 Colony a replica 1 PGCGROWTHCONDITIONS
Treatment A Population 2 Colony a replica 2 PGCGROWTHCONDITIONS
Treatment A Population 2 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment A Population 2 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment A Population 2 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment A Population 2 Colony c replica 2 PGCGROWTHCONDITIONS
Treatment B Population 3 Colony a replica 1 PGCGROWTHCONDITIONS
Treatment B Population 3 Colony a replica 2 PGCGROWTHCONDITIONS
Treatment B Population 3 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment B Population 3 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment B Population 3 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment B Population 3 Colony c replica 2 PGCGROWTHCONDITIONS
Treatment B Population 4 Colony a replica 1 PGCGROWTHCONDITIONS
Treatment B Population 4 Colony a replica 2 PGCGROWTHCONDITIONS
Treatment B Population 4 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment B Population 4 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment B Population 4 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment B Population 4 Colony c replica 2 PGCGROWTHCONDITIONS
Treatment B Population 5 Colony a replica 1 PGCGROWTHCONDITIONS
Treatment B Population 5 Colony a replica 2 PGCGROWTHCONDITIONS
Treatment B Population 5 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment B Population 5 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment B Population 5 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment B Population 5 Colony c replica 2 PGCGROWTHCONDITIONS
Treatment C Population 6 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment C Population 6 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment C Population 6 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment C Population 6 Colony c replica 2 PGCGROWTHCONDITIONS
Treatment C Population 7 Colony b replica 1 PGCGROWTHCONDITIONS
Treatment C Population 7 Colony b replica 2 PGCGROWTHCONDITIONS
Treatment C Population 7 Colony c replica 1 PGCGROWTHCONDITIONS
Treatment C Population 7 Colony c replica 2 PGCGROWTHCONDITIONS
100ng 16S rRNA gene amplicon of a mock community PGCGROWTHCONDITIONS
Bacteroides fragilis PGCGROWTHCONDITIONS
Blautia coccoides PGCGROWTHCONDITIONS
[Clostridium] leptum PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Faecal samples were collected by the Department of Microbiology and Alimentary Pharmabiotic Centre (Cork, Ireland) from three elderly patients (176, 204 and 205). The mock community was performed after culture of each individual bacterial strain in their reference medium at their optimal temperature for several days. PGCGROWTHCONDITIONS
Lactobacillus acidophilus PGCGROWTHCONDITIONS
Mock community PGCGROWTHCONDITIONS
No treatment were studied in this experience PGCGROWTHCONDITIONS
Pixel intensities were extracted using the “Feature Extraction” software (Agilent Technologies, Palo Alto, CA). No normalization step was performed and the retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals. PGCGROWTHCONDITIONS
sample type: mock community [artificial bacterial DNA mix] PGCGROWTHCONDITIONS
Total DNA was extracted from three human faecal samples using  Qiagen’s DNA Stool Kit (Qiagen, West Sussex, UK). Total genomic DNA was extracted from pure bacterial cultures using DNeasy Blood and Tissue Kit (Qiagen, West Sussex, UK). 10ng of sample was then used for PCR amplification. 16S rRNA genes were amplified using universal primers 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACT). PCR reactions were performed in a 50µl volume, using DreamTaq DNA polymerase (Fermentas, St. Leon-Rot, Germany). The PCR reaction consisted of an initial denaturation step at 95°C for 5min followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 58°C for 40 s and elongation at 72°C for 2 min. A final extension step was performed at 72°C for 5 min. PCR product size was verified by electrophoresis with 1% (w PGCGROWTHCONDITIONS
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
genotype: plasmid cured strain PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Isolated from feces of a HUS patient from an outbreak in China in 1999 PGCGROWTHCONDITIONS
plasmid cured rep1 PGCGROWTHCONDITIONS
plasmid cured rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Xuzhou21 PGCGROWTHCONDITIONS
strain: Xuzhou21m PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2). PGCGROWTHCONDITIONS
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively. PGCGROWTHCONDITIONS
The gene expression was calculated using the RPKM method PGCGROWTHCONDITIONS
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially. PGCGROWTHCONDITIONS
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols. PGCGROWTHCONDITIONS
WT rep1 PGCGROWTHCONDITIONS
WT rep2 PGCGROWTHCONDITIONS
Xuzhou21 cured of the pO157_Sal plasmid PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
BL21_1 PGCGROWTHCONDITIONS
BL21_2 PGCGROWTHCONDITIONS
Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g PGCGROWTHCONDITIONS
condition: LB+3g PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the IlluminaHiSeq platform. PGCGROWTHCONDITIONS
Genome_build: gi|387825439 PGCGROWTHCONDITIONS
genotype: Pck over-expressed PGCGROWTHCONDITIONS
genotype: wild-type PGCGROWTHCONDITIONS
PCK over PGCGROWTHCONDITIONS
Raw sequencing reads (FASTQ)were processed by Xpression and only the uniquely mapped reads were subjected to further analysis. PGCGROWTHCONDITIONS
Reference files for the genome sequence being queried, Escherichia coli BL21(DE3) genome (NC_012971) were uploaded. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BL21(DE3) PGCGROWTHCONDITIONS
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads. PGCGROWTHCONDITIONS
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification. PGCGROWTHCONDITIONS
Xpression (https: PGCGROWTHCONDITIONS
Xpression was used for filtering and trimming reads. PGCGROWTHCONDITIONS
control 12h PGCGROWTHCONDITIONS
control 24h PGCGROWTHCONDITIONS
control 6h PGCGROWTHCONDITIONS
Cy3 and Cy5 intensities were normalized by scaling so that the 75th percentile in the Cy3 and Cy5 channels were equal. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
expose Bacillus VOC 12h PGCGROWTHCONDITIONS
Expose Bacillus VOC-12h rep1 PGCGROWTHCONDITIONS
Expose Bacillus VOC-12h rep2 PGCGROWTHCONDITIONS
Expose Bacillus VOC-12h rep3 PGCGROWTHCONDITIONS
Expose Bacillus VOC-12h rep4 PGCGROWTHCONDITIONS
expose Bacillus VOC24h PGCGROWTHCONDITIONS
Expose Bacillus VOC-24h rep1 PGCGROWTHCONDITIONS
Expose Bacillus VOC-24h rep2 PGCGROWTHCONDITIONS
Expose Bacillus VOC-24h rep3 PGCGROWTHCONDITIONS
Expose Bacillus VOC-24h rep4 PGCGROWTHCONDITIONS
expose Bacillus VOC 6h PGCGROWTHCONDITIONS
Expose Bacillus VOC-6h rep1 PGCGROWTHCONDITIONS
Expose Bacillus VOC-6h rep2 PGCGROWTHCONDITIONS
Expose Bacillus VOC-6h rep3 PGCGROWTHCONDITIONS
Expose Bacillus VOC-6h rep4 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
time: 12 h PGCGROWTHCONDITIONS
time: 24 h PGCGROWTHCONDITIONS
time: 6 h PGCGROWTHCONDITIONS
Total RNAs were extracted using RNeasy mini kit (Qiagen, #74104) following manufacture's instruction PGCGROWTHCONDITIONS
treatment: Bacillus volatile organic compounds (VOCs) PGCGROWTHCONDITIONS
treatment: control PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_minus_aMG_1 PGCGROWTHCONDITIONS
CV108_minus_aMG_2 PGCGROWTHCONDITIONS
CV108_minus_aMG_3 PGCGROWTHCONDITIONS
CV108_plus_aMG_1 PGCGROWTHCONDITIONS
CV108_plus_aMG_2 PGCGROWTHCONDITIONS
CV108_plus_aMG_3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy1-[CV104_pHDB3_5.txt] PGCGROWTHCONDITIONS
Galaxy2-[CV104_pLCV1_5.txt] PGCGROWTHCONDITIONS
Galaxy3-[CV104_pLCV1_10.txt] PGCGROWTHCONDITIONS
Galaxy4-[CV104_pHDB3_20.txt] PGCGROWTHCONDITIONS
Galaxy5-[CV104_pLCV1_20.txt] PGCGROWTHCONDITIONS
Galaxy6-[CV104_pHDB3_10.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3) PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
genotype: Galaxy1-[CV104_pHDB3_5] PGCGROWTHCONDITIONS
genotype: Galaxy2-[CV104_pLCV1_5] PGCGROWTHCONDITIONS
genotype: Galaxy3-[CV104_pLCV1_10] PGCGROWTHCONDITIONS
genotype: Galaxy4-[CV104_pHDB3_20] PGCGROWTHCONDITIONS
genotype: Galaxy5-[CV104_pLCV1_20] PGCGROWTHCONDITIONS
genotype: Galaxy6-[CV104_pHDB3_10] PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
genotype: pHDB3 PGCGROWTHCONDITIONS
genotype: pLCV1 PGCGROWTHCONDITIONS
genotype: SgrR PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% 2-DG PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
MG1655-aMG_1 PGCGROWTHCONDITIONS
MG1655+aMG_1 PGCGROWTHCONDITIONS
MG1655-aMG_2 PGCGROWTHCONDITIONS
MG1655+aMG_2 PGCGROWTHCONDITIONS
MG1655-aMG_3 PGCGROWTHCONDITIONS
MG1655+aMG_3 PGCGROWTHCONDITIONS
MG1655_minus_aMG_1 PGCGROWTHCONDITIONS
MG1655_minus_aMG_2 PGCGROWTHCONDITIONS
MG1655_minus_aMG_3 PGCGROWTHCONDITIONS
MG1655_plus_aMG_1 PGCGROWTHCONDITIONS
MG1655_plus_aMG_2 PGCGROWTHCONDITIONS
MG1655_plus_aMG_3 PGCGROWTHCONDITIONS
pHDB3_1 PGCGROWTHCONDITIONS
pHDB3_2 PGCGROWTHCONDITIONS
pHDB3_3 PGCGROWTHCONDITIONS
pLCV1_1 PGCGROWTHCONDITIONS
pLCV1_2 PGCGROWTHCONDITIONS
pLCV1_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http: PGCGROWTHCONDITIONS
SgrR_1 PGCGROWTHCONDITIONS
SgrR_2 PGCGROWTHCONDITIONS
SgrR_3 PGCGROWTHCONDITIONS
sgrS_T_1 PGCGROWTHCONDITIONS
sgrS_T_2 PGCGROWTHCONDITIONS
sgrS_T_3 PGCGROWTHCONDITIONS
sgrS_un_1 PGCGROWTHCONDITIONS
sgrS_un_2 PGCGROWTHCONDITIONS
sgrS_un_3 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_1 PGCGROWTHCONDITIONS
WT_2 PGCGROWTHCONDITIONS
WT_3 PGCGROWTHCONDITIONS
WT_minus_2DG_1 PGCGROWTHCONDITIONS
WT_minus_2DG_2 PGCGROWTHCONDITIONS
WT_minus_2DG_3 PGCGROWTHCONDITIONS
WT_plus_2DG_1 PGCGROWTHCONDITIONS
WT_plus_2DG_2 PGCGROWTHCONDITIONS
WT_plus_2DG_3 PGCGROWTHCONDITIONS
wt_T_1 PGCGROWTHCONDITIONS
wt_T_2 PGCGROWTHCONDITIONS
wt_T_3 PGCGROWTHCONDITIONS
wt_un_1 PGCGROWTHCONDITIONS
wt_un_2 PGCGROWTHCONDITIONS
wt_un_3 PGCGROWTHCONDITIONS
Chemostat 1 h irradiated PGCGROWTHCONDITIONS
Chemostat 1h irradiated PGCGROWTHCONDITIONS
Chemostat 50 h irradiated PGCGROWTHCONDITIONS
Control chemostat 1 h not irradiated PGCGROWTHCONDITIONS
Control chemostat 1h not irradiated PGCGROWTHCONDITIONS
Control chemostat 50 h not irradiated PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Jaguar PGCGROWTHCONDITIONS
UVA irradiated chemostat for 1 h, run 1 PGCGROWTHCONDITIONS
UVA irradiated chemostat for 1 h, run 2 PGCGROWTHCONDITIONS
UVA irradiated chemostat for 1 h, run 2 dye swap PGCGROWTHCONDITIONS
UVA irradiated chemostat for 1 h, run 3 PGCGROWTHCONDITIONS
UVA irradiated chemostat for 50 h, run 1 PGCGROWTHCONDITIONS
UVA irradiated chemostat for 50 h, run 2 PGCGROWTHCONDITIONS
UVA irradiated chemostat for 50 h, run 3 PGCGROWTHCONDITIONS
e.coli culture protocol: conditioned Caco-2 cell medium PGCGROWTHCONDITIONS
e.coli culture protocol: fresh medium PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
STEC EC472 PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in conditioned medium, replicate 1 [COND] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in conditioned medium, replicate 2 [COND] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in conditioned medium, replicate 3 [COND] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in conditioned medium, replicate 4 [COND] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in fresh medium, replicate 1 [FRESH] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in fresh medium, replicate 2 [FRESH] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in fresh medium, replicate 3 [FRESH] PGCGROWTHCONDITIONS
STEC EC472 after 3 hrs incubation in fresh medium, replicate 4 [FRESH] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in conditioned medium, replicate 1 [COND] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in conditioned medium, replicate 2 [COND] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in conditioned medium, replicate 3 [COND] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in conditioned medium, replicate 4 [COND] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in fresh medium, replicate 1 [FRESH] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in fresh medium, replicate 2 [FRESH] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in fresh medium, replicate 3 [FRESH] PGCGROWTHCONDITIONS
STEC EH41 after 3 hrs incubation in fresh medium, replicate 4 [FRESH] PGCGROWTHCONDITIONS
STEC EH41, conditioned medium PGCGROWTHCONDITIONS
STEC EH41, fresh medium PGCGROWTHCONDITIONS
STEC strains were lysate using lysozyme (1 mg PGCGROWTHCONDITIONS
strain: EC472 PGCGROWTHCONDITIONS
strain: EH41 (isolated from patient with HUS) PGCGROWTHCONDITIONS
The conditioned medium (C) was the DMEM medium containing 10% FBS without antibiotics recovered after 24 hrs incubation with differentiated Caco-2 cells. 400 µL of STEC culture were inoculated in 4 mL of C medium and incubated for 3 hrs at 37°C. After this period the bacteria were recovered by centrifugation for 10 min at 5000 xg and the pellet was ressuspended in 600 µL of RNAprotect Bacteria Reagent (Qiagen cat. no. 76506, Valencia, CA) for RNA extraction. PGCGROWTHCONDITIONS
The fresh medium (F) was the DMEM medium containing 10% FBS without antibiotics. 400 µL of STEC culture were inoculated in 4 mL of F medium and incubated for 3 hrs at 37°C. After this period the bacteria were recovered by centrifugation for 10 min at 5000 xg and the pellet was ressuspended in 600 µL of RNAprotect Bacteria Reagent (Qiagen cat. no. 76506, Valencia, CA) for RNA extraction. PGCGROWTHCONDITIONS
The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 020097_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities but not included the normalization process.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. PGCGROWTHCONDITIONS
antibody: polycolonal antiserum was raised against His6-ArcA then Affinity Purified against ArcA to yield the polyclonal antibodies used for ChIP PGCGROWTHCONDITIONS
ArcA - Aerobic - Affinity Purified - A PGCGROWTHCONDITIONS
ArcA - Anaerobic - Affinity Purified - biological rep A PGCGROWTHCONDITIONS
ArcA - Anaerobic - Affinity Purified -biological rep B PGCGROWTHCONDITIONS
∆ArcA - Anaerobic - Affinity Purified - technical rep A PGCGROWTHCONDITIONS
∆ArcA - Anaerobic - Affinity Purified - technical rep B PGCGROWTHCONDITIONS
ArcA INPUT DNA from WT Escherchia coli MG1655 K-12, no antibody control PGCGROWTHCONDITIONS
ArcA INPUT from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
∆arcA IP DNA from PK9416 PGCGROWTHCONDITIONS
ArcA IP DNA from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
ArcA IP from WT Escherichia coli MG1655 K-12 PGCGROWTHCONDITIONS
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown aerobically (25% O2, 70% N2 and 5% CO2) until mid-log phase (OD600 of 0.35) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
INPUT ChIP DNA from PK9416, no ArcA control PGCGROWTHCONDITIONS
strain: MG1655 K-12 WT PGCGROWTHCONDITIONS
strain: PK9416 PGCGROWTHCONDITIONS
10 ng of DNA were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 400 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  Single read, 75 bp (rep A) or 36 bp (rep B) runs were performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx.   Basecalling was performed using the standard Illumina Pipeline version 1.6. PGCGROWTHCONDITIONS
Anaerobic Cultures PGCGROWTHCONDITIONS
antibody: polyclonal antiserum was raised against His6-ArcA then Affinity Purified using purified ArcA to yield the polyclonal antibodies used for ChIP PGCGROWTHCONDITIONS
ArcA_anaerobic_ChIP-seq_IP_A.wig: U00096.2 PGCGROWTHCONDITIONS
ArcA_anaerobic_ChIP-seq_IP_B.wig: U00096.2 PGCGROWTHCONDITIONS
ArcA IP ChIP-seq Anaerobic Biological replicate 1 PGCGROWTHCONDITIONS
ArcA IP ChIP-seq Anaerobic Biological replicate 2 PGCGROWTHCONDITIONS
Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
culture condition: Anaerobic Cultures PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
genome build: U00096.2 PGCGROWTHCONDITIONS
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads. PGCGROWTHCONDITIONS
strain: Wild Type K-12 PGCGROWTHCONDITIONS
BL21(DE3)_adhE mutant PGCGROWTHCONDITIONS
BL21(DE3), adhE mutant PGCGROWTHCONDITIONS
B strain_wild type PGCGROWTHCONDITIONS
B strain, wild type PGCGROWTHCONDITIONS
BW25113_adhE mutant PGCGROWTHCONDITIONS
BW25113, adhE mutant PGCGROWTHCONDITIONS
Data quantification was performed using Agilent Feature Extraction software 9.3.2.1 (Agilent Technology, USA). The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3.1 (Agilent Technology, USA). Normalization for Agilent one-color method was performed, which is Data transformation. Set measurements less than 5.0 to 5.0 and Per Chip : Normalize to 50th percentage. Reliable genes were filtered by flag as following the Agilent manual. PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For control and test RNAs, the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling Kit, one color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2ug total RNA was mixed with WT primer mix and incubated at 65ºC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40ºC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70ºC for 15min. PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
K-12 strain_wild type PGCGROWTHCONDITIONS
K-12 strain, wild type PGCGROWTHCONDITIONS
strain background: B PGCGROWTHCONDITIONS
strain background: K-12 PGCGROWTHCONDITIONS
The E. coli strains were grown for six hours under anaerobic growth condition in glucose-containing complex medium. PGCGROWTHCONDITIONS
The microarray experiment was performed with two serotypes of wild type E. coli and their adhE mutants: (1) K-12 strain, wild type; (2) B strain, wild type; (3) BW25113, adhE mutants; (4) BL21(DE3), adhE mutants. PGCGROWTHCONDITIONS
A single large fastq  format file of high quality reads (Q ≥ 30) was split into about 10 smaller files by using a shell script splitReads.sh PGCGROWTHCONDITIONS
CASAVA version 1.4 PGCGROWTHCONDITIONS
Cells were cultured in LB medium containing ampicillin at 28˚C. The overnight cell culture was inoculated into the fresh  medium at 1 PGCGROWTHCONDITIONS
Each type of error rates per position was determined as  the number of sequence reads with a particular type of base-substitution  divided by the number of the reads with the reference base in each DNA  position. PGCGROWTHCONDITIONS
E.coli strain MG1655 PGCGROWTHCONDITIONS
error-prone in vitro (Mn2+) PGCGROWTHCONDITIONS
error-prone in vitro MnCl2 PGCGROWTHCONDITIONS
error-proof in vitro 1 (GreAB PGCGROWTHCONDITIONS
error-proof in vitro 2 (GreAB PGCGROWTHCONDITIONS
error-proof in vitro MgCl2 +GreAB PGCGROWTHCONDITIONS
error-proof in vitro MnCl2 +GreAB PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: pPR9 plasmid (ref is Kashlec et al., 1989, PMID: 2547695) PGCGROWTHCONDITIONS
In vitro RNA preparation: The 5.7 kb RNA was purified from the digested DNA, NTPs, abortive oligo-RNA products, and proteins by Acidic phenol extraction, G50 spin column, followed by EtOH precipitation. PGCGROWTHCONDITIONS
in vivo PGCGROWTHCONDITIONS
In vivo RNA preparation: The cells in 200 ml culture were harvested and resuspended with a solution containing 0.5% SDS, 20 mM sodium acetate (pH 5.5), and 10 mM EDTA. The suspended cells were mixed with an equal volume of pre-warmed saturated phenol (20 mM sodium acetate, 10 mM EDTA pH 5.5) and incubated for 5 min at 60  C. The mixture was centrifuged, and RNA and DNA were precipitated with ethanol from the supernatant. The pellet was dissolved in DNase I buffer with 10U of DNaseI and incubated for 30 min. RNA was separated from the digested DNA by acidic phenol extraction followed by G-50 Micro column (GE Healthcare) purification, and then precipitated with ethanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis. PGCGROWTHCONDITIONS
mRNA-seq with barcode (Illumina  TruSeq Index 1-5) PGCGROWTHCONDITIONS
mrna synthesis: in vitro MgCl2 PGCGROWTHCONDITIONS
mrna synthesis: in vitro MgCl2 +GreAB PGCGROWTHCONDITIONS
mrna synthesis: in vitro MnCl2 PGCGROWTHCONDITIONS
mrna synthesis: in vitro MnCl2 +GreAB PGCGROWTHCONDITIONS
mrna synthesis: in vivo PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
standard in vitro (Mg2+) PGCGROWTHCONDITIONS
standard in vitro MgCl2 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text file of transition error rate per position. The position is corresponding to the position of \Sequenced region of pPR9 plasmid\ (one of the attached txt file). PGCGROWTHCONDITIONS
The cells culture were harvested and resuspended with a  solution containing 0.5% SDS, 20 mM sodium acetate (pH 5.5), and 10 mM  EDTA. The suspended cells were mixed with an equal volume of pre-warmed  saturated phenol (20 mM sodium acetate, 10 mM EDTA pH 5.5) and incubated  for 5 min at 60˚C. PGCGROWTHCONDITIONS
The numbers of 4 bases A, T, G, C, and N were counted in each position of the mapped reads by using the program  SAMtools 0.1.18 with supplemental use of a Perl script. PGCGROWTHCONDITIONS
The obtained reads were aligned  and mapped to the pPR9 plasmid DNA sequences using   Bowtie 0.12.7. PGCGROWTHCONDITIONS
We established a method for preparing five different cDNA  libraries each with its own barcode for Illumina sequencing. Each 6-nt barcode allows multiplexing all five in vitro and  in vivo preparations in a single sequencing analysis. our method introduces internal control sequences to the library  that are subjected to the artifact errors, but are not for RNAP  errors. The 5’ fragment of the 5.7 kb RNA  transcripts was reverse transcribed to make the cDNA.  The cDNA was subjected to PCR reactions that generated  six  200 bp segments. The primers contained a specific barcode  for each of the five starting preparations and the inner Illuminasequencing  adapters. The 2nd-step of PCR generated  the final cDNA libraries for the Illumina sequencing by using  the 1st-step PCR product as a template and primers containing  the outer sequencing adapters in the 5’ tails. PGCGROWTHCONDITIONS
At the appropriate phase of growth, a one-eighth volume of stop solution (95% [v PGCGROWTHCONDITIONS
E. coli batch culture without TAP PGCGROWTHCONDITIONS
E. coli batch culture with TAP PGCGROWTHCONDITIONS
E. coli - TAP PGCGROWTHCONDITIONS
E. coli + TAP PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
Escherichia coli K12 strain BW25113 (Datsenko & Wanner 2000. PNAS 97: 6640) was cultivated in 100 mL of LB broth ( Miller 1972. In: Experiments in molecular genetics. Cold Spring Harbor Laboratory, NY) in a 250 mL Erlenmeyer flask at 37°C with shaking (250 rpm) to an O.D.600nm of 0.6. S. coelicolor A3(2) strain M145 (Kieser et al. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich.) was incubated in YEME broth (Kieser et al. 2000) at 30°C with shaking until the mycelia became pigmented. PGCGROWTHCONDITIONS
For each of the 4 libraries (2 bacterial samples x 2 treatments), we counted the number of times each nucleotide position was the first in a sequence read using a simple script (unpubl. resource). The forward and reverse strands were then processed separately. PGCGROWTHCONDITIONS
Genome_build: The reference genomes used for E. coli K12 strain BW25113 and S. coelicolor A3(2) strain M145 were U00096.2 and AL645882, respectively. PGCGROWTHCONDITIONS
genotype: wild-type PGCGROWTHCONDITIONS
Libraries were constructed by vertis Biotechnologie AG, Germany (www.vertis-biotech.com) as a service that included treating an aliquot of each RNA sample with TAP. The 5'-sequencing adaptor was ligated to transcripts prior to fragmentation, thereby allowing the 5' ends of both long and short transcripts to be detected. Each of the 4 libraries was constructed using a different barcode. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA sequences from each of the two differential analyses were processed and mapped to the corresponding genomes as a service provided by vertis Biotechnologie AG, Germany (www.vertis-biotech.com). This involved trimming adaptor sequence and masking for low-quality sequence. PGCGROWTHCONDITIONS
RNA was isolated from the pellet of E. coli cells using a well-established, published protocol (Kime et al. 2008. In RNA Turnover in Bacteria, Archaea and Organelles, Vol 447 (ed. LE Maquat, CM Arraiano), pp. 215). The cell pellet of S. coelicolor was resuspended in Kirby mix (Kieser et al. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich.), 100 µL per 1 O.D.600nm unit, and transferred to Lysing Matrix B tubes containing fine silica beads (MP Biomedical). Tubes were then placed in a high-speed benchtop homogenizer (Fastprep-24, MP Biomedical; set at 6.5 M PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BedGraphs of the reads before and after TAP treatment for each of the samples. Separate files are provided for the forward and reverse strands. PGCGROWTHCONDITIONS
The sample sources of individual reads were determined by the barcoding. The barcodes for the minus and plus TAP treatments were ACTTGA and CGATGT, respectively, for the E. coli RNA, and CAGATC and ATCACG, respectively, for the S. coelicolor RNA. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
treatment: tobacco acid pyrophosphatase (TAP) PGCGROWTHCONDITIONS
Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug PGCGROWTHCONDITIONS
chip antibody: anti-c-myc antibody PGCGROWTHCONDITIONS
chip antibody: anti-FecI antibody PGCGROWTHCONDITIONS
chip antibody: anti-RpoB antibody PGCGROWTHCONDITIONS
chip antibody: anti-RpoD antibody PGCGROWTHCONDITIONS
chip antibody: anti-RpoF antibody PGCGROWTHCONDITIONS
chip antibody: anti-RpoN antibody PGCGROWTHCONDITIONS
chip antibody: anti-RpoS antibody PGCGROWTHCONDITIONS
chip antibody manufacturer: Upstate PGCGROWTHCONDITIONS
chip antibody: normal mouse IgG (Upstate) PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of RNAP and DNA was immunoprecipitated by anti-RpoB antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of RNAP and DNA was immunoprecipitated by using normal mouse IgG for the control. PGCGROWTHCONDITIONS
E. Coli Exponential FecI ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential FecI ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential FecI ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Exponential FecI ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential FecI ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential FecI ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoB ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoB ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoB ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoB ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoB ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoB ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD DelN ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD DelN ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD DelN ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoD DelN ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoF ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoF ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoF ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoF ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoF ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoF ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoH ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoH ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoH ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoH ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoN ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoN ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoN ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoN ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoN ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoN ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. Coli Exponential RpoS ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoS ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Exponential RpoS ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Exponential RpoS ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoB ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoB ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoB ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoB ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoD ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoD ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoD ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoD ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoN ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoN ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoN ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Glutamine RpoN ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoB ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoB ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoB ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoB ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoD ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoD ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoD ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoD ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoH ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoH ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoH ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoH ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoH ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Heatshock RpoH ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. Coli Iron RpoD ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Iron RpoD ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Iron RpoD ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Iron RpoD ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoB ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoB ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoB ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoB ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD DelS ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD DelS ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD DelS ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoD DelS ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoS ChIP DNA 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoS ChIP DNA 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoS ChIP DNA 3 PGCGROWTHCONDITIONS
E. Coli Stationary RpoS ChIP DNA Mock 1 PGCGROWTHCONDITIONS
E. Coli Stationary RpoS ChIP DNA Mock 2 PGCGROWTHCONDITIONS
E. Coli Stationary RpoS ChIP DNA Mock 3 PGCGROWTHCONDITIONS
E. coli strains  were grown in minimal M9 medium supplemented with glucose (2 g PGCGROWTHCONDITIONS
E. coli strains  were grown in minimal W2 medium supplemented with glucose (2 g PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype: rpoH-8myc PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
genotype: ΔrpoN PGCGROWTHCONDITIONS
genotype: ΔrpoS PGCGROWTHCONDITIONS
The raw pair data (.txt file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at mid-log phase (OD600nm 0.5) in M9 glucose (0.2%) media, with 42oC heatshock for 10 min. PGCGROWTHCONDITIONS
Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS
Cells at stationary phase (OD600nm 1.5) in M9 glucose media PGCGROWTHCONDITIONS
E. coli glutamine 1 PGCGROWTHCONDITIONS
E. coli glutamine 2 PGCGROWTHCONDITIONS
E. coli heatshock 1 PGCGROWTHCONDITIONS
E. coli heatshock 2 PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
E. coli stationary 1 PGCGROWTHCONDITIONS
E. coli stationary 2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: glutamine PGCGROWTHCONDITIONS
treatment: heat shock PGCGROWTHCONDITIONS
treatment: stationary phase PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
35381_1 PGCGROWTHCONDITIONS
35382_2 PGCGROWTHCONDITIONS
DNA were extracted and purified as described by Muniesa et al. (2003). Shiga toxin 2-converting bacteriophages associated with clonal variability in Escherichia coli O157:H7 strains of human origin isolated from a single outbreak. Infect Immun 71, 4554-4562. PGCGROWTHCONDITIONS
E. coli 3538 #1 PGCGROWTHCONDITIONS
E. coli 3538 #2 PGCGROWTHCONDITIONS
ecoli_3538_2x_v2 PGCGROWTHCONDITIONS
E. coli 3538 #3 PGCGROWTHCONDITIONS
ecoli_3538_3x_v2 PGCGROWTHCONDITIONS
ecoli_3538_4x_v2 PGCGROWTHCONDITIONS
E. coli D1 #1 PGCGROWTHCONDITIONS
E. coli D1 #2 PGCGROWTHCONDITIONS
ecoli_D1_2x_v2 PGCGROWTHCONDITIONS
E. coli D1 #3 PGCGROWTHCONDITIONS
ecoli_D1_3x_v2 PGCGROWTHCONDITIONS
ecoli_D1_4x_v2 PGCGROWTHCONDITIONS
E. coli EDL933 #1  PGCGROWTHCONDITIONS
E. coli EDL933 #2 PGCGROWTHCONDITIONS
ecoli_EDL933_2x_v2 PGCGROWTHCONDITIONS
E. coli EDL933 #3 PGCGROWTHCONDITIONS
ecoli_EDL933_3x_v2 PGCGROWTHCONDITIONS
ecoli_EDL933_4x_v2 PGCGROWTHCONDITIONS
E. coli K-12 W3110 #1 PGCGROWTHCONDITIONS
E. coli K-12 W3110 #2 PGCGROWTHCONDITIONS
E. coli K-12 W3110 #3 PGCGROWTHCONDITIONS
E. coli phage 3538 #1 PGCGROWTHCONDITIONS
E. coli phage 3538 #2 PGCGROWTHCONDITIONS
ecoli_W3110_2x_v2 PGCGROWTHCONDITIONS
ecoli_W3110_3x_v2 PGCGROWTHCONDITIONS
ecoli_W3110_4x_v2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Induced from E. coli strain 3538 with mitomycin C PGCGROWTHCONDITIONS
Isolate W3110 of K-12 strain PGCGROWTHCONDITIONS
overnight in Luria-Bertani (LB) broth with continuous agitation PGCGROWTHCONDITIONS
phage DNA PGCGROWTHCONDITIONS
Qiagen Genomic Tip 500 PGCGROWTHCONDITIONS
serotype O157:H7 PGCGROWTHCONDITIONS
serotype O157:H7  PGCGROWTHCONDITIONS
serotype O175:H16 PGCGROWTHCONDITIONS
Standard Affymetrix procedure PGCGROWTHCONDITIONS
40 hours 1 PGCGROWTHCONDITIONS
40 hours 2 PGCGROWTHCONDITIONS
40 hours 3 PGCGROWTHCONDITIONS
40 hours cultivation in continuous culture (mineral medium with 100 mg PGCGROWTHCONDITIONS
40 hours of cultivation in continuous colture (mineral medium with 100 mg PGCGROWTHCONDITIONS
500 hours 1 PGCGROWTHCONDITIONS
500 hours 2 PGCGROWTHCONDITIONS
500 hours 3 PGCGROWTHCONDITIONS
500 hours of cultivation in continuous colture (mineral medium with 100 mg PGCGROWTHCONDITIONS
Batch growth in mineral medium supplied with 4 g PGCGROWTHCONDITIONS
control PGCGROWTHCONDITIONS
Control PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Sample PGCGROWTHCONDITIONS
The data provided are the original data generated with the Jaguar software from the microarray images. The VALUEs reported represent log10 (Cy5 PGCGROWTHCONDITIONS
Cells used for expression analysis were grown in minimal medium (Glansdorff, 1965) supplemented with 0.5% glucose (w PGCGROWTHCONDITIONS
E.Coli, strain P4XB2 mutant, grown in presence of arginine(100 ug PGCGROWTHCONDITIONS
E.Coli, strain P4X, grown in presence of arginine(100 ug PGCGROWTHCONDITIONS
E.Coli, strain P4X, grown on minimal medium, reference sample PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Initial data analysis was performed using the GeneChip® Operating Software. Microarray quality control parameters were as follow: noise (RawQ) less than 5, background signal less than 40 (100 target intensity for array scaling), consistent numbers of genes detected as present across arrays. PGCGROWTHCONDITIONS
P4XB2 Mutant (1992) in Arginine PGCGROWTHCONDITIONS
P4XB2 Mutant (1993) in Arginine PGCGROWTHCONDITIONS
P4XB2 Mutant (1994) in Arginine PGCGROWTHCONDITIONS
P4X Wild Type (1753) Reference PGCGROWTHCONDITIONS
P4X Wild Type (1754) in Arginine PGCGROWTHCONDITIONS
P4X Wild Type (1765) Reference PGCGROWTHCONDITIONS
P4X Wild Type (1766) in Arginine PGCGROWTHCONDITIONS
P4X Wild Type (1989) Reference PGCGROWTHCONDITIONS
P4X Wild Type (1990) in Arginine PGCGROWTHCONDITIONS
Strain P4X, grown on minimal medium, reference sample PGCGROWTHCONDITIONS
Total RNA was isolated using a RNeasy® RNA isolation kit, according to the manufacturer’s specifications (QIAGEN, Germany) and stored in RNase-free water at –80°C. RNA concentration was determined by UV-spectrometry and its quality controlled by agarose gel electrophoresis. PGCGROWTHCONDITIONS
BW25113-pCA24N PGCGROWTHCONDITIONS
BW25113-pCA24N_dosP PGCGROWTHCONDITIONS
Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104). PGCGROWTHCONDITIONS
Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice. PGCGROWTHCONDITIONS
Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
overexpression of dosP (pCA24N_dosP) PGCGROWTHCONDITIONS
overexpression of empty vector (pCA24N) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Strains were grown in LBCm30 at 37°C with shaking at 250 rpm.  16 h overnight cultures were diluted at 1:1000 into fresh LBCm30, grown to OD600 ~ 1.0, and induced with 1 mM IPTG for 90 min. PGCGROWTHCONDITIONS
1-butanol was added at a final concentration of 0.9% (vol PGCGROWTHCONDITIONS
A0-A1_rep1_a PGCGROWTHCONDITIONS
A0-A1_rep1_b PGCGROWTHCONDITIONS
A0-A1_rep2_a PGCGROWTHCONDITIONS
A0-A1_rep2_b PGCGROWTHCONDITIONS
A0-A1_rep3_a PGCGROWTHCONDITIONS
A0-A1_rep3_b PGCGROWTHCONDITIONS
A0-E0_rep1_a PGCGROWTHCONDITIONS
A0-E0_rep1_b PGCGROWTHCONDITIONS
A0-E0_rep2_a PGCGROWTHCONDITIONS
A0-E0_rep2_b PGCGROWTHCONDITIONS
A0-E0_rep3_a PGCGROWTHCONDITIONS
A0-E0_rep3_b PGCGROWTHCONDITIONS
Background correction and normalization (print-tip loess and quantile) were performed using the limma R package. PGCGROWTHCONDITIONS
Cells were grown aerobically in 50 ml LB medium until OD600 reached ~1 (late log phase). PGCGROWTHCONDITIONS
E0-E1_rep1_a PGCGROWTHCONDITIONS
E0-E1_rep1_b PGCGROWTHCONDITIONS
E0-E1_rep2_a PGCGROWTHCONDITIONS
E0-E1_rep2_b PGCGROWTHCONDITIONS
E0-E1_rep3_a PGCGROWTHCONDITIONS
E0-E1_rep3_b PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
mutant E. coli, after butanol treatment PGCGROWTHCONDITIONS
mutant E. coli, before butanol treatment PGCGROWTHCONDITIONS
protocol: late log phase, LB PGCGROWTHCONDITIONS
protocol: late log phase, LB, 30 min after butanol treatment PGCGROWTHCONDITIONS
Qiagen Rneasy column PGCGROWTHCONDITIONS
strain: KCTC 2571 PGCGROWTHCONDITIONS
strain: PKH5000 PGCGROWTHCONDITIONS
wt E. coli, after butanol treatment PGCGROWTHCONDITIONS
wt E. coli, before butanol treatment PGCGROWTHCONDITIONS
Algorithm: ExpressionStat 5.0 (Affymetrix Microarray Suite Version 5.0) PGCGROWTHCONDITIONS
APEC strain O08 PGCGROWTHCONDITIONS
APEC strain SCI-07 PGCGROWTHCONDITIONS
Escherichia coli O08 PGCGROWTHCONDITIONS
Escherichia coli SCI-07 PGCGROWTHCONDITIONS
growth media: DMEM growth media PGCGROWTHCONDITIONS
RNA was extracted using RNAeasy mini-Kit Qiagen and hybridizated on Affymatrix microarrays. PGCGROWTHCONDITIONS
strain: APEC SCI-07 (O nontypeable:H31) isolated from lesions (gelatinous edema) on the skin of the head and periorbital tissues from a laying hen showing clinical signs of swollen head syndrome PGCGROWTHCONDITIONS
strain: O08 (O38:H10) obtained from the yolk of the abdomen of a diseased 1-day-old chick PGCGROWTHCONDITIONS
Two Avian Pathogenic Escherichia coli strains (APEC) were grown at 37°C in Dulbecco´s Modified Eagle´s Media (DMEM) media until reach O.D 600 = 0.8. PGCGROWTHCONDITIONS
culture PGCGROWTHCONDITIONS
E. coli cells_HS15min PGCGROWTHCONDITIONS
E. coli cells_HS30min PGCGROWTHCONDITIONS
E. coli cells_HS60min PGCGROWTHCONDITIONS
E. coli cells_LB(OD=0.87) PGCGROWTHCONDITIONS
E. coli cells_M-P0h PGCGROWTHCONDITIONS
E. coli cells_M-P2h PGCGROWTHCONDITIONS
E. coli cells_M-P4h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS15min_r1_HiSeq PGCGROWTHCONDITIONS
HS15min_r2_HiSeq PGCGROWTHCONDITIONS
HS15min_r3_GAII PGCGROWTHCONDITIONS
HS30min_r1_HiSeq PGCGROWTHCONDITIONS
HS30min_r2_HiSeq PGCGROWTHCONDITIONS
HS60min_r1_HiSeq PGCGROWTHCONDITIONS
HS60min_r2_HiSeq PGCGROWTHCONDITIONS
LB(OD=0.87) PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P0h_r1_HiSeq PGCGROWTHCONDITIONS
M-P0h_r2_HiSeq PGCGROWTHCONDITIONS
M-P2h_r1_HiSeq PGCGROWTHCONDITIONS
M-P2h_r2_HiSeq PGCGROWTHCONDITIONS
M-P4h_r1_HiSeq PGCGROWTHCONDITIONS
M-P4h_r2_HiSeq PGCGROWTHCONDITIONS
M-P4h_r3_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
basal media: M9 + 4 g PGCGROWTHCONDITIONS
cra KO PGCGROWTHCONDITIONS
cra KO + L-trp PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log_cra KO_glc minimal media_aerobic PGCGROWTHCONDITIONS
Mid log_cra KO_glc minimal media + L-tryptophan_aerobic PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_mntR KO_glc minimal media_aerobic PGCGROWTHCONDITIONS
Mid log_mntR KO_glc minimal media_anaerobic PGCGROWTHCONDITIONS
Mid log_nac KO_glc minimal media + adenine_aerobic PGCGROWTHCONDITIONS
Mid log_nac KO_glc minimal media_aerobic PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media + adenine_aerobic PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_aerobic rep1 PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_aerobic rep2 PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_aerobic rep3 PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_anaerobic rep1 PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_anaerobic rep2 PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_anaerobic rep3 PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media + L-tryptophan_aerobic PGCGROWTHCONDITIONS
mntR KO PGCGROWTHCONDITIONS
mntR KO -O2 PGCGROWTHCONDITIONS
nac KO PGCGROWTHCONDITIONS
nac KO + ade PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
oxygen condition: anaerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: adenine (10 mM) PGCGROWTHCONDITIONS
supplementation: L-tryptophan (20 mg PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT + ade PGCGROWTHCONDITIONS
WT + L-trp PGCGROWTHCONDITIONS
WT -O2 PGCGROWTHCONDITIONS
23A1 PGCGROWTHCONDITIONS
23B1 PGCGROWTHCONDITIONS
23C3 PGCGROWTHCONDITIONS
39A1 PGCGROWTHCONDITIONS
39B1 PGCGROWTHCONDITIONS
39C1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
WTA1 PGCGROWTHCONDITIONS
WTB1 PGCGROWTHCONDITIONS
WTC3 PGCGROWTHCONDITIONS
Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 10^8 cells PGCGROWTHCONDITIONS
condition: osmotic pressure PGCGROWTHCONDITIONS
condition: regular PGCGROWTHCONDITIONS
condition: starvation PGCGROWTHCONDITIONS
condition: temperature change PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure NaCl 0.20 M PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.20 M PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure NaCl 0.20 M, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.20 M, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.20 M, rep 3 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.45 M PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.45 M, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.45 M, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.45 M, rep 3 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.55 M PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.55 M, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.55 M, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, osmotic pressure, NaCl 0.55 M, rep 3 PGCGROWTHCONDITIONS
E. coli MDS42, regular PGCGROWTHCONDITIONS
E. coli MDS42, regular, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, regular, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, regular, rep 3 PGCGROWTHCONDITIONS
E. coli MDS42, starvation, SHX 100 ng PGCGROWTHCONDITIONS
E. coli MDS42, starvation, SHX 150 ng PGCGROWTHCONDITIONS
E. coli MDS42, starvation, SHX 50 ng PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 40.0 deg C PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 40.0 deg C, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 40.0 deg C, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 40.0 deg C, rep 3 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.5 deg C PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.5 deg C, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.5 deg C, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.5 deg C, rep 3 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.8 deg C PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.8 deg C, rep 1 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.8 deg C, rep 2 PGCGROWTHCONDITIONS
E. coli MDS42, temperature change, 41.8 deg C, rep 3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). PGCGROWTHCONDITIONS
strain: MDS42 PGCGROWTHCONDITIONS
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions. PGCGROWTHCONDITIONS
Control Wild type E.coli SE15 vs. LuxS mutant E.coli SE15 PGCGROWTHCONDITIONS
E.coli SE15 is cultured in LB broth and LuxS E.coli SE15 is cultured in LB broth with kanamycine at 37℃and in 150rpm shaking incubator PGCGROWTHCONDITIONS
E.coli SE15 is isolated from indwelling catheter of patient and deleted LuxS gene (related to quorum sensing) PGCGROWTHCONDITIONS
E.coli SE15 isolated from indwelling catheter of patient PGCGROWTHCONDITIONS
Escherichia coli SE15 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Genowiz 4.0.5.6 normalized, background subtracted data obtained from log2 of processed Red signal PGCGROWTHCONDITIONS
strain: SE15 PGCGROWTHCONDITIONS
Total RNA extracted using Trizol following manufacturer's instructions PGCGROWTHCONDITIONS
Wild type E.coli SE15 vs. LuxS mutant E.coli SE15 PGCGROWTHCONDITIONS
Agilent Feature Extraction Software version 10.5.1.1. PGCGROWTHCONDITIONS
chip antibody: Anti-FLAG (sigma-aldrich cat no F3165) PGCGROWTHCONDITIONS
chip antibody: none, input PGCGROWTHCONDITIONS
chip antibody: normal rabbit IgG (Upstate Biotechnology, Cat. no. 12-370) PGCGROWTHCONDITIONS
CSH50 control E-minimal medium 90 min PGCGROWTHCONDITIONS
CSH50 control (mock igG) E-minimal medium replicate 1 PGCGROWTHCONDITIONS
CSH50 control (mock igG) E-minimal medium replicate 2 PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 4.5 90 min PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 4.5 90 min replicate 1 PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 4.5 90 min replicate 2 PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 4.5 90 min replicate 3 PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 7 90 min PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 7 90 min replicate 1 PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 7 90 min replicate 2 PGCGROWTHCONDITIONS
CSH50 E-minimal medium pH 7 90 min replicate 3 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
OD600 15 units of cells were harvested for each ChIP procedure. Cells were harvested by centrifugation at 4,000 rpm for 8 min at room temperature and resuspended in 50 ml of pre-warmed PBS (37°C) in a 250 ml flask. DNA-protein and protein-protein interactions were cross-linked by adding 1,351 µl of formaldehyde drop-wise to a final concentration of 1%. Samples were cross-linked at room temperature with stirring for 30 min. Glycine was added to a final concentration of 0.125 M with stirring for 5 min at room temperature. Cells were centrifuged at 4,000 rpm for 8 min at 4°C and the supernatant removed. The pellet was re-suspended in 0.6 ml of lysis buffer containing 50 mM Tris-HCl, 10 mM EDTA, 1% SDS and incubated on ice for 10 min. 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Strains were grown overnight in LB broth and then equalised to 0.15 optical density (OD600nm) units. Cells were collected and washed in EG minimal medium (pH 7.2). This wash step was repeated twice more with centrifugation to collect the cells. The final pellet was resuspended in 1 ml of 1X EG minimal (pH 7.2). Cells were grown to OD600 ~0.5-0.6 in a 40 ml volume in a 250 ml flask at 37°C and 200 rpm. PGCGROWTHCONDITIONS
The culture was divided into two 20-ml volumes and the cells collected by centrifugation. The supernatant was removed and the two pellets were subjected to different treatments. One was resuspended in 1 ml of pre-warmed 1X EG-minimal medium pH 7.2. The second was resuspended in 1 ml of pre-warmed 1X EG-minimal medium pH 4.5. Each suspension was added to a final volume of 20 ml 1X EG minimal medium of the same pH in a 250 ml flask. Cells were grown at 37°C and 200 rpm shaking for 90 min before harvesting for analysis. PGCGROWTHCONDITIONS
5 ml bacterial cultures with a known inoculum of E. coli cells (1.0 × 109 cfu PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
E. coli treated with bicontinious microemulsion PGCGROWTHCONDITIONS
E. coli treated with o PGCGROWTHCONDITIONS
E. coli treated with w PGCGROWTHCONDITIONS
E. coli without microemulsion treatment PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Raw microarray intensity data were normalized per chip to the same mean value, which is recommended by the manufacturer. PGCGROWTHCONDITIONS
strain: CMCC(B) 44102 PGCGROWTHCONDITIONS
The strain E. coli CMCC(B) 44102, was provided by Institute of Microbiology, Chinese Academy of Sciences and preserved at the Department of Food Science and Nutrition, Zhejiang University. The strain was maintained in nutrient agar medium (NA, Hangzhou Microbiological Agents Co., Ltd., China) at 37 °C, and cultured in tryptic soy broth (TSB, Qingdao Hope Biotechnology Co., Ltd., China) at pH 7.0 and transferred every 20-24 h with incubation at 37 °C. PGCGROWTHCONDITIONS
Total RNA from cells of the microemulsion-treated E. coli was extracted in duplicate using an RNAiso Plus (Cat. # 908, Takara, Japan) according to the manufacturer’s instructions, PGCGROWTHCONDITIONS
treatment: bicontinious microemulsion PGCGROWTHCONDITIONS
treatment: control PGCGROWTHCONDITIONS
treatment: oil in water PGCGROWTHCONDITIONS
treatment: water in oil PGCGROWTHCONDITIONS
Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 0.1L PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 40min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 80min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 10min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 20min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 40min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 80min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 10min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 20min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 2.5min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 for 5min PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 31_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 33_Aerobic culture_CO gas_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 37_Aerobic culture_CO gas_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 39_Anaerobic culture_CO gas_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 53_Anaerobic culture_CO gas_biol rep 3_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 10 2 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 55_Anaerobic culture_CO gas_biol rep 3_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 56_Anaerobic culture_CO gas_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
strain: Wild type strain MG1655 PGCGROWTHCONDITIONS
time: 10min PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
time: 20min PGCGROWTHCONDITIONS
time: 2.5min PGCGROWTHCONDITIONS
time: 40min PGCGROWTHCONDITIONS
time: 5min PGCGROWTHCONDITIONS
time: 80min PGCGROWTHCONDITIONS
Total RNA extracted using Trizol following manufacturer's instructions PGCGROWTHCONDITIONS
treatment: Continuous aerobically grown cultures in Evans medium, exposed to 0.1L PGCGROWTHCONDITIONS
treatment: Continuous aerobically grown cultures in Evans medium, exposed to 40uM CORM-3 PGCGROWTHCONDITIONS
treatment: Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 PGCGROWTHCONDITIONS
treatment: Continuous anaerobically grown cultures in Evans medium, exposed to 40uM CORM-3 PGCGROWTHCONDITIONS
treatment: Continuous anaerobically grown cultures in Evans medium, exposed to CO gas at 0.1L PGCGROWTHCONDITIONS
E.coli, grown in LB+glycerol to 0.8OD PGCGROWTHCONDITIONS
E.coli, grown in LB to 0.8OD PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli was grown aerobically in Luria-Bertani (LB) broth and LB + glycerol at 30°C in an incubator shaker at 150 r.p.m. PGCGROWTHCONDITIONS
growth protocol: grown in LB+glycerol to 0.8OD PGCGROWTHCONDITIONS
growth protocol: grown in LB to 0.8OD PGCGROWTHCONDITIONS
LB, biological rep1 PGCGROWTHCONDITIONS
LB, biological rep2 PGCGROWTHCONDITIONS
LB, biological rep3 PGCGROWTHCONDITIONS
LB+glycerol, biological rep1 PGCGROWTHCONDITIONS
LB+glycerol, biological rep2 PGCGROWTHCONDITIONS
LB+glycerol, biological rep3 PGCGROWTHCONDITIONS
RNA was isolated from the culture by using the Qiagen RNeasy mini-prep kit.cDNA was synthesized using 5-10 µg PGCGROWTHCONDITIONS
The  intensity cell files were then imported, normalized for background correction (used RMA for normalization)and data analysed using Gene Spring 11.5 software. PGCGROWTHCONDITIONS
To study gene expression,  28 days old E.coli cells were grown in the presence of LB broth and LB broth supplemented with 10% v PGCGROWTHCONDITIONS
chip antibody: anti-FLAG antibody (Sigma Cat #: F3165-1MG) PGCGROWTHCONDITIONS
chip antibody: none PGCGROWTHCONDITIONS
ChIP_hns-F_bcm-#1 PGCGROWTHCONDITIONS
ChIP_hns-F_bcm+#1 PGCGROWTHCONDITIONS
ChIP_hns-F_bcm-#2 PGCGROWTHCONDITIONS
ChIP_hns-F_bcm+#2 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
consensus binding regions were obtained as the portion which was covered by replicate samples PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each co-ordinate coverage was calculated as the number of reads which was aligned againist the position. The coverage was normalized and converted into a z score. Z score threshold of 12 was selected to identify H-NS binding regions. PGCGROWTHCONDITIONS
genome build: ASM584v1 PGCGROWTHCONDITIONS
H-NS flag tagged cells with bcm treatment PGCGROWTHCONDITIONS
H-NS flag tagged cells without bcm treatment PGCGROWTHCONDITIONS
Input_hns-F_bcm-#1 PGCGROWTHCONDITIONS
Input_hns-F_bcm+#1 PGCGROWTHCONDITIONS
Input_hns-F_bcm-#2 PGCGROWTHCONDITIONS
Input_hns-F_bcm+#2 PGCGROWTHCONDITIONS
MG1655 hns-FLAG cells were grown in liquid LB medium with and without bicyclomycin (BCM) at 37 degree with shaking at 200rpm PGCGROWTHCONDITIONS
reads aligned to the reference genome of E. coli K-12 Mg1655 using BWA, with quality threshold of 20 PGCGROWTHCONDITIONS
Reads mapped to more than one locus were discarded. The mapped position obtained from the SAM output file from BWA lists was taken and the position was extended to 280 bp which is the average length of DNA fragments submitted for sequencing. PGCGROWTHCONDITIONS
Standard illumina library construction protocol for ChIP PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: contents : reference seq,co-ordinate start position,co-ordinate end position,counts for the position, mapping quality, strand position PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: format:bed format PGCGROWTHCONDITIONS
The binding regions were considered by taking into account base position with z-score greater than threshold and merging adjacent binding regions seperated by a distance of less than 200bo into the single binding regions PGCGROWTHCONDITIONS
Two biological replicates were performed for samples with and without treatment with bicyclomycin. For samples without BCM treatment, cells were grown OD600 ≈ 0.8 at 370 with shaking at 200 rpm.  For samples with BCM treatment, cells were grown to early log phase (O.D. 600=0.1) ≈ 1h at 370 with shaking at 200 rpm. BCM was added to a final concentration of 25ug mL-1 PGCGROWTHCONDITIONS
2xOriT PGCGROWTHCONDITIONS
A2, osmotolerant mutant PGCGROWTHCONDITIONS
A2 Replicate 1 PGCGROWTHCONDITIONS
A2 Replicate 2 PGCGROWTHCONDITIONS
A4, osmotolerant mutant PGCGROWTHCONDITIONS
A4 Replicate 1 PGCGROWTHCONDITIONS
A4 Replicate 2 PGCGROWTHCONDITIONS
average fitness: 0.196851676684606 PGCGROWTHCONDITIONS
average fitness: 0.296737932583603 PGCGROWTHCONDITIONS
average fitness: 0.344592279464807 PGCGROWTHCONDITIONS
average fitness: 0.353076289611459 PGCGROWTHCONDITIONS
average fitness: 0.434286415079969 PGCGROWTHCONDITIONS
average fitness: 0.502711019240335 PGCGROWTHCONDITIONS
Data were normalized using the LOWESS algorithm and analyzed for statistical significance using the MeV package PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
G2, osmotolerant mutant PGCGROWTHCONDITIONS
G2 Replicate 1 PGCGROWTHCONDITIONS
G2 Replicate 2 PGCGROWTHCONDITIONS
G3, osmotolerant mutant PGCGROWTHCONDITIONS
G3 Replicate 1 PGCGROWTHCONDITIONS
G3 Replicate 2 PGCGROWTHCONDITIONS
G5, osmotolerant mutant PGCGROWTHCONDITIONS
G5 Replicate 1 PGCGROWTHCONDITIONS
G5 Replicate 2 PGCGROWTHCONDITIONS
G6, osmotolerant mutant PGCGROWTHCONDITIONS
G6 Replicate 1 PGCGROWTHCONDITIONS
G6 Replicate 2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Grown in glucose M9 media supplemented with 0.55 M NaCl PGCGROWTHCONDITIONS
Hfr-2xSFX- PGCGROWTHCONDITIONS
population: A2 PGCGROWTHCONDITIONS
population: A4 PGCGROWTHCONDITIONS
population: G2 PGCGROWTHCONDITIONS
population: G3 PGCGROWTHCONDITIONS
population: G5 PGCGROWTHCONDITIONS
population: G6 PGCGROWTHCONDITIONS
Samples were grown to mid exponential phase (OD approx 0.5). Cultures were then harvested with rapid filtration and resuspended in RNALater to stop RNA degradation. The Zymo Quick-RNA miniprep kit was used to extract pure RNA for subsequent analysis PGCGROWTHCONDITIONS
strain description: E. coli BW25113 with an integrated F tra operon at the trp locus, plus additional F oriT sequences integrated at mbhA and hyfC PGCGROWTHCONDITIONS
strain description: E. coli BW25113 with F oriTs integrated at mbhA and hyfC PGCGROWTHCONDITIONS
strain: unevolved parent strain PGCGROWTHCONDITIONS
All samples were extracted using the Qiagen Rnasey Mini Kit, following standard protocol PGCGROWTHCONDITIONS
cDNA libraries were constructed at Purdue using an adapted SOLiD Total RNA-Seq Kit. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard SOLiD 4 Total RNA-Seq protocol. RNA-seq via SOLiD 4 sequencing of libraries prepared by ligation based chemistry to provide strand-specific datasets. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
For alignment of the SAET reads to the E. coli MG1655 reference genome (RefSeq NC_000913), the short read alignment tool Bowtie ver. 1.8 (Langmead, et al., PMID 19261174) was utilized in three consecutive passes for each sample dataset. For the first pass, we use paired end color space mapping with a distance cutoff of 350 bases between read mates. Bowtie parameters were set to include only perfect matches and suppress reads that map to more than one genome location, i.e., uniquely mapped reads are retained. In practice we found the efficiency of paired end mapping was between 3 and 10%. To improve the overall alignment we mapped the orphan 5’ and 3’ end reads in two additional passes with Bowtie. The output of the three passes through Bowtie was three SAM files for each sample. Overall, we achieved 40-60% mapping efficiency with this three-pass strategy. PGCGROWTHCONDITIONS
Genome_build: ASM584v1; Reference genome for E. coli MG1655 (RefSeq NC_000913). Paper title:Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 PGCGROWTHCONDITIONS
phase of growth: 15 min post stationary PGCGROWTHCONDITIONS
phase of growth: 180 min post stationary PGCGROWTHCONDITIONS
phase of growth: 30 min post stationary PGCGROWTHCONDITIONS
phase of growth: Late log phase OD 1.6 PGCGROWTHCONDITIONS
phase of growth: Log phase OD 0.1 PGCGROWTHCONDITIONS
phase of growth: Log phase OD 0.2 PGCGROWTHCONDITIONS
phase of growth: Log phase OD 0.3 PGCGROWTHCONDITIONS
phase of growth: Log phase OD 0.4 PGCGROWTHCONDITIONS
phase of growth: Log phase OD 0.8 PGCGROWTHCONDITIONS
phase of growth: Log phase OD 1.4 PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rna treatment: no RNA treatment PGCGROWTHCONDITIONS
rna treatment: rRNA depleted PGCGROWTHCONDITIONS
rna treatment: rRNA depleted; Terminal Exonuclease PGCGROWTHCONDITIONS
rpoS_04_rep1 PGCGROWTHCONDITIONS
rpoS_04_rep2 PGCGROWTHCONDITIONS
rpoS_04_TEX PGCGROWTHCONDITIONS
rpoS_15min_rep1 PGCGROWTHCONDITIONS
rpoS_16_rep1 PGCGROWTHCONDITIONS
rpoS_180min_rep1 PGCGROWTHCONDITIONS
rpoS_30min_rep1 PGCGROWTHCONDITIONS
rpoS_30min_rep2 PGCGROWTHCONDITIONS
rpoS_30min_TEX PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (WIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand WIG files). First, the script reads in the paired-end BAM file and counts the nucleotides spanning inserts between the mated 5’ and 3’ reads. Next, the script pulls in the orphan 5’ and 3’ reads from the respective BAM files and increments the base counts at each base location without duplicating the reads already incremented from the paired ends. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
sub strain: BW38028 PGCGROWTHCONDITIONS
sub strain: BW39452 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: WIG files are provided showing uniquely mapped sequence reads (normalized). PGCGROWTHCONDITIONS
The raw data output (XSEQ files) from the SOLiD 4 Genetic Analyzer System are passed through the ABI Sequence Accuracy Enhancement Tool (SAET) PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie and convert them to BAM format. PGCGROWTHCONDITIONS
WIG files were normalized by using an in-house script that reads in the raw WIG files while excluding counts from all 22 rRNA genes. A simple global normalization approach was utilized that multiplied the count at each base location by 1 billion and divides that value by the sum of base counts at all base locations in the file. This normalization strategy is anlogous to the Total Count approach used for normalizing gene-specific read alignments. In this way, the base counts are expressed as parts per billion. PGCGROWTHCONDITIONS
WIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source in a 2L B. Braun Biostat® B fermenter with working volume of 1 L MOPS minimal medium with 0.2% glucose, at 37°C, pH was kept constant at 7.4 by the addition of 1 M NaOH, and dissolved oxygen was maintained above 40% of saturation by adjusting the agitation speeds in the range of 270–500 rpm with fixed 1.5 liter PGCGROWTHCONDITIONS
WT_01_rep1 PGCGROWTHCONDITIONS
WT_02_rep1 PGCGROWTHCONDITIONS
WT_03_rep1 PGCGROWTHCONDITIONS
WT_04_rep1 PGCGROWTHCONDITIONS
WT_04_rep2 PGCGROWTHCONDITIONS
WT_04-R_rep1 PGCGROWTHCONDITIONS
WT_04_TEX PGCGROWTHCONDITIONS
WT_08_rep1 PGCGROWTHCONDITIONS
WT_14_rep1 PGCGROWTHCONDITIONS
WT_15min_rep1 PGCGROWTHCONDITIONS
WT_16_rep1 PGCGROWTHCONDITIONS
WT_16-R_rep1 PGCGROWTHCONDITIONS
WT_180min_rep1 PGCGROWTHCONDITIONS
WT_30min_rep1 PGCGROWTHCONDITIONS
WT_30min_rep2 PGCGROWTHCONDITIONS
WT_30min-R_rep1 PGCGROWTHCONDITIONS
WT_30min_TEX PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genomic dna PGCGROWTHCONDITIONS
genomic DNA PGCGROWTHCONDITIONS
MG1655, SD197,SB227,SF301 and SS046 PGCGROWTHCONDITIONS
MG1655,SD197,SB227,SF301 and SS046 PGCGROWTHCONDITIONS
ration of median(635 PGCGROWTHCONDITIONS
Ratio of median PGCGROWTHCONDITIONS
reference DNA PGCGROWTHCONDITIONS
SB10_1 PGCGROWTHCONDITIONS
SB10_2 PGCGROWTHCONDITIONS
SB10_3 PGCGROWTHCONDITIONS
SB1_1 PGCGROWTHCONDITIONS
SB11_1 PGCGROWTHCONDITIONS
SB11_2 PGCGROWTHCONDITIONS
SB11_3 PGCGROWTHCONDITIONS
SB1_2 PGCGROWTHCONDITIONS
SB12_1 PGCGROWTHCONDITIONS
SB12_2 PGCGROWTHCONDITIONS
SB12_3 PGCGROWTHCONDITIONS
SB1_3 PGCGROWTHCONDITIONS
SB13_1 PGCGROWTHCONDITIONS
SB13_2 PGCGROWTHCONDITIONS
SB13_3 PGCGROWTHCONDITIONS
SB14_1 PGCGROWTHCONDITIONS
SB14_2 PGCGROWTHCONDITIONS
SB14_3 PGCGROWTHCONDITIONS
SB15_1 PGCGROWTHCONDITIONS
SB15_2 PGCGROWTHCONDITIONS
SB15_3 PGCGROWTHCONDITIONS
SB16_1 PGCGROWTHCONDITIONS
SB16_2 PGCGROWTHCONDITIONS
SB16_3 PGCGROWTHCONDITIONS
SB17_1 PGCGROWTHCONDITIONS
SB17_2 PGCGROWTHCONDITIONS
SB17_3 PGCGROWTHCONDITIONS
SB18_1 PGCGROWTHCONDITIONS
SB18_2 PGCGROWTHCONDITIONS
SB18_3 PGCGROWTHCONDITIONS
SB1 genomic DNA PGCGROWTHCONDITIONS
SB2_1 PGCGROWTHCONDITIONS
SB2_2 PGCGROWTHCONDITIONS
SB2_3 PGCGROWTHCONDITIONS
SB3_1 PGCGROWTHCONDITIONS
SB3_2 PGCGROWTHCONDITIONS
SB3_3 PGCGROWTHCONDITIONS
SB5_1 PGCGROWTHCONDITIONS
SB5_2 PGCGROWTHCONDITIONS
SB5_3 PGCGROWTHCONDITIONS
SB6_1 PGCGROWTHCONDITIONS
SB6_2 PGCGROWTHCONDITIONS
SB6_3 PGCGROWTHCONDITIONS
SB7_1 PGCGROWTHCONDITIONS
SB7_2 PGCGROWTHCONDITIONS
SB7_3 PGCGROWTHCONDITIONS
SB8_1 PGCGROWTHCONDITIONS
SB8_2 PGCGROWTHCONDITIONS
SB8_3 PGCGROWTHCONDITIONS
SB9_1 PGCGROWTHCONDITIONS
SB9_2 PGCGROWTHCONDITIONS
SB9_3 PGCGROWTHCONDITIONS
SD10_1 PGCGROWTHCONDITIONS
SD10_2 PGCGROWTHCONDITIONS
SD10_3 PGCGROWTHCONDITIONS
SD11_1 PGCGROWTHCONDITIONS
SD11_2 PGCGROWTHCONDITIONS
SD11_3 PGCGROWTHCONDITIONS
SD12_1 PGCGROWTHCONDITIONS
SD12_2 PGCGROWTHCONDITIONS
SD12_3 PGCGROWTHCONDITIONS
SD13_1 PGCGROWTHCONDITIONS
SD13_2 PGCGROWTHCONDITIONS
SD13_3 PGCGROWTHCONDITIONS
SD2_1 PGCGROWTHCONDITIONS
SD2_2 PGCGROWTHCONDITIONS
SD2_3 PGCGROWTHCONDITIONS
SD3_1 PGCGROWTHCONDITIONS
SD3_2 PGCGROWTHCONDITIONS
SD3_3 PGCGROWTHCONDITIONS
SD4_1 PGCGROWTHCONDITIONS
SD4_2 PGCGROWTHCONDITIONS
SD4_3 PGCGROWTHCONDITIONS
SD5_1 PGCGROWTHCONDITIONS
SD5_2 PGCGROWTHCONDITIONS
SD5_3 PGCGROWTHCONDITIONS
SD6_1 PGCGROWTHCONDITIONS
SD6_2 PGCGROWTHCONDITIONS
SD6_3 PGCGROWTHCONDITIONS
SD7_1 PGCGROWTHCONDITIONS
SD7_2 PGCGROWTHCONDITIONS
SD7_3 PGCGROWTHCONDITIONS
SD8_1 PGCGROWTHCONDITIONS
SD8_2 PGCGROWTHCONDITIONS
SD8_3 PGCGROWTHCONDITIONS
SD9_1 PGCGROWTHCONDITIONS
SD9_2 PGCGROWTHCONDITIONS
SD9_3 PGCGROWTHCONDITIONS
SF1a_1 PGCGROWTHCONDITIONS
SF1a_2 PGCGROWTHCONDITIONS
SF1a_3 PGCGROWTHCONDITIONS
SF1b_1 PGCGROWTHCONDITIONS
SF1b_2 PGCGROWTHCONDITIONS
SF1b_3 PGCGROWTHCONDITIONS
SF2b_1 PGCGROWTHCONDITIONS
SF2b_2 PGCGROWTHCONDITIONS
SF2b_3 PGCGROWTHCONDITIONS
SF3_1 PGCGROWTHCONDITIONS
SF3_2 PGCGROWTHCONDITIONS
SF3_3 PGCGROWTHCONDITIONS
SF4a_1 PGCGROWTHCONDITIONS
SF4a_2 PGCGROWTHCONDITIONS
SF4a_3 PGCGROWTHCONDITIONS
SF4b_1 PGCGROWTHCONDITIONS
SF4b_2 PGCGROWTHCONDITIONS
SF4b_3 PGCGROWTHCONDITIONS
SF5_2 PGCGROWTHCONDITIONS
SF5_3 PGCGROWTHCONDITIONS
SF6_1 PGCGROWTHCONDITIONS
SF6_2 PGCGROWTHCONDITIONS
SF6_3 PGCGROWTHCONDITIONS
SFx_2 PGCGROWTHCONDITIONS
SFx_3 PGCGROWTHCONDITIONS
SFy_1 PGCGROWTHCONDITIONS
SFy_2 PGCGROWTHCONDITIONS
SFy_3 PGCGROWTHCONDITIONS
Shigella boydii PGCGROWTHCONDITIONS
Shigella boydii 13 PGCGROWTHCONDITIONS
Shigella boydii 14 PGCGROWTHCONDITIONS
Shigella boydii 15 PGCGROWTHCONDITIONS
Shigella boydii  15 PGCGROWTHCONDITIONS
Shigella boydii 16 PGCGROWTHCONDITIONS
Shigella boydii 17 PGCGROWTHCONDITIONS
Shigella boydii 18 PGCGROWTHCONDITIONS
Shigella boydii serogroup 1 PGCGROWTHCONDITIONS
Shigella boydii serogroup 2 PGCGROWTHCONDITIONS
Shigella boydii serotype 1 PGCGROWTHCONDITIONS
Shigella boydii serotype 10 PGCGROWTHCONDITIONS
Shigella boydii serotype 11 PGCGROWTHCONDITIONS
Shigella boydii serotype 12 PGCGROWTHCONDITIONS
Shigella boydii serotype 13 PGCGROWTHCONDITIONS
Shigella boydii serotype2 PGCGROWTHCONDITIONS
Shigella boydii serotype 2 PGCGROWTHCONDITIONS
Shigella boydii serotype3 PGCGROWTHCONDITIONS
Shigella boydii serotype 3 PGCGROWTHCONDITIONS
Shigella boydii serotype 5 PGCGROWTHCONDITIONS
Shigella boydii serotype 6 PGCGROWTHCONDITIONS
Shigella boydii  serotype 7 PGCGROWTHCONDITIONS
Shigella boydii serotype 7 PGCGROWTHCONDITIONS
Shigella boydii serotype 8 PGCGROWTHCONDITIONS
Shigella boydii serotype 9 PGCGROWTHCONDITIONS
Shigella dysenteriae PGCGROWTHCONDITIONS
Shigella dysenteriae 10 PGCGROWTHCONDITIONS
Shigella dysenteriae 11 PGCGROWTHCONDITIONS
Shigella dysenteriae 12 PGCGROWTHCONDITIONS
Shigella dysenteriae 13 PGCGROWTHCONDITIONS
Shigella dysenteriae 2 PGCGROWTHCONDITIONS
Shigella dysenteriae 3 PGCGROWTHCONDITIONS
Shigella dysenteriae 4 PGCGROWTHCONDITIONS
Shigella dysenteriae 5 PGCGROWTHCONDITIONS
Shigella dysenteriae 6 PGCGROWTHCONDITIONS
Shigella dysenteriae 7 PGCGROWTHCONDITIONS
Shigella dysenteriae 8 PGCGROWTHCONDITIONS
Shigella dysenteriae 9 PGCGROWTHCONDITIONS
Shigella flexneri PGCGROWTHCONDITIONS
Shigella flexneri 1a PGCGROWTHCONDITIONS
Shigella flexneri 1b PGCGROWTHCONDITIONS
Shigella flexneri 2b PGCGROWTHCONDITIONS
Shigella flexneri 3 PGCGROWTHCONDITIONS
Shigella flexneri 4a PGCGROWTHCONDITIONS
Shigella flexneri 4b PGCGROWTHCONDITIONS
Shigella flexneri 5 PGCGROWTHCONDITIONS
Shigella flexneri 6 PGCGROWTHCONDITIONS
Shigella flexneri variant x PGCGROWTHCONDITIONS
Shigella flexneri variant y PGCGROWTHCONDITIONS
All cultures were carried out in a 5 l fermentor BIOSTAT B-DCU (Sartorius BBI Systems Inc. Melsungen) at controlled temperature 37°C, pH 7.0, and dissolved oxygen tension 30%. The culture volume was 2 l. All reagents were purchased from Sigma-Aldrich, Inc. The synthetic culture medium had the following composition (g l-1): 8, glucose; 14.6, K2HPO4; 3.6, NaH2PO4·H2O; 2.68, (NH4)2SO4; 2, Na2SO4; 1, MgSO4; 1, Na-citrate; 0.5, NH4Cl; 2 ml of 10 mg l-1 of thiamine; 3 ml of trace element solution (g l-1 20.0, Na-EDTA; 15.0, FeCl3·6H2O; 0.5, CaCl2·2H2O; 0.2, ZnSO4·7H2O; 0.2, CoCl2·6H2O; 0.2, CuSO4·5H2O; 0.2, MnSO4·4H2O). The chemostat culture was performed with adding feed medium PGCGROWTHCONDITIONS
BL21 PGCGROWTHCONDITIONS
BL21 (mu=0.20) (1) PGCGROWTHCONDITIONS
BL21 (mu=0.20) (2) PGCGROWTHCONDITIONS
BL21 (mu=0.20) (3) PGCGROWTHCONDITIONS
BL21 (mu=0.20) (4) PGCGROWTHCONDITIONS
BL21(mu=0.46) (1) PGCGROWTHCONDITIONS
BL21(mu=0.46) (2) PGCGROWTHCONDITIONS
BL21(mu=0.46) (3) PGCGROWTHCONDITIONS
BL21(mu=0.46) (4) PGCGROWTHCONDITIONS
E. coli samples for RNA extraction were taken during fermentation. Cells were harvested by centrifugation at the cultivation temperature (37°C, 10,000 g, 1 min), separated from the supernatant, and rapidly frozen in dry ice. The samples were stored at -70°C until analysis PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli BL21 PGCGROWTHCONDITIONS
Escherichia coli BL21 (mu=0.20) PGCGROWTHCONDITIONS
Escherichia coli BL21 (mu=0.46) PGCGROWTHCONDITIONS
Expression data were analyzed with the Microarray Analysis Suite, version 5.0  (Affymetrix). Global scaling was performed to compare genes between chips. Each chip was normalized to a target intensity value of 2,500. Expression analysis files created by Microarray Suite, version 5.0, were exported to Microsoft Excel for data formatting. PGCGROWTHCONDITIONS
Genotype: F- ompT hsdSB(rB-mB-) gal dcm (DE3) PGCGROWTHCONDITIONS
Trizol extraction of total RNA was performed according to the manufacturer's instructions PGCGROWTHCONDITIONS
Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 10^8 cells PGCGROWTHCONDITIONS
condition: 37ºC PGCGROWTHCONDITIONS
condition: 45ºC PGCGROWTHCONDITIONS
E. coli Type_II genotype strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli Type_II genotype strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli Type_II genotype strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli Type_II genotype strain, under 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli Type_II genotype strain, under 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli Type_II genotype strain, under 45ºC, rep 3 PGCGROWTHCONDITIONS
E. coli Type_III genotype strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli Type_III genotype strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli Type_III genotype strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli Type_III genotype strain, under 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli Type_III genotype strain, under 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli Type_III genotype strain, under 45ºC, rep 3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). PGCGROWTHCONDITIONS
strain: DH1ΔleuB::gfpuv5-kmr PGCGROWTHCONDITIONS
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 7,000 × g for 3 min at 4°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions. PGCGROWTHCONDITIONS
Cells were centrifuged and the cell pellets were stored in RNA Later solution at -80ºC. The RNeasy Mini Kit (Qiagen, Venlo, Netherlands) was used to isolate total RNA. The samples were then incubated at 37ºC with RNaseOut (New England Biolabs) and DNaseI (New England Biolabs) according to the manufacture’s protocol for 1 hour. The samples were mixed with saturated phenol PGCGROWTHCONDITIONS
E. coli MG1655-C8-1 PGCGROWTHCONDITIONS
E. coli MG1655-C8-3 PGCGROWTHCONDITIONS
E. coli MG1655-control-1 PGCGROWTHCONDITIONS
E. coli MG1655-control-2 PGCGROWTHCONDITIONS
E. coli MG1655-control-3 PGCGROWTHCONDITIONS
E. coli MG1655-MOPS+2%Dextrose PGCGROWTHCONDITIONS
E. coli MG1655-MOPS+2%Dextrose+10mM C8 PGCGROWTHCONDITIONS
E. coli MG1655 was grown in MOPS + 2 % Dextrose minimal media +- 10 mM octanoic acid (pH=7.0) from OD550 0.05 to ~0.8 and harvested at Midlog. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
MATLAB v. R2012b program using GCRMA algorithm PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The treatment condition includes adding 10 mM octanoic acid during logarithmic growth. PGCGROWTHCONDITIONS
As described in description PGCGROWTHCONDITIONS
As described in the description PGCGROWTHCONDITIONS
E. coli K12 grown in minimal medium with added 5 μM TPEN PGCGROWTHCONDITIONS
E. coli K12 grown in minimal medium without added TPEN PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
mRNA PGCGROWTHCONDITIONS
Transcriptional response of E. coli to TPEN (m1) PGCGROWTHCONDITIONS
Transcriptional response of E. coli to TPEN (m2) PGCGROWTHCONDITIONS
Transcriptional response of E. coli to TPEN (m3) PGCGROWTHCONDITIONS
Transcriptional response of E. coli to TPEN (t1) PGCGROWTHCONDITIONS
Transcriptional response of E. coli to TPEN (t2) PGCGROWTHCONDITIONS
Transcriptional response of E. coli to TPEN (t3) PGCGROWTHCONDITIONS
All cultures were based on MOPS media with 0.2% glucose (Teknova), with either full supplement (Neidhardt et al., 1974). An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 2.8-liter flask at 37C with aeration (180 rpm) until OD600 reached 0.3. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, D. Burkhardt, C.A. Gross, J. S. Weissman (Cell). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
EC_Cont1_DNA PGCGROWTHCONDITIONS
EC_Cont1_RNA PGCGROWTHCONDITIONS
EC_Cont2_DNA PGCGROWTHCONDITIONS
EC_Cont2_RNA PGCGROWTHCONDITIONS
EC_Trim1_DNA PGCGROWTHCONDITIONS
EC_Trim1_RNA PGCGROWTHCONDITIONS
EC_Trim2_DNA PGCGROWTHCONDITIONS
EC_Trim2_RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For all the samples; when 1 PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2) PGCGROWTHCONDITIONS
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1) PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Illumina Casava 1.8 software was used for basecalling. PGCGROWTHCONDITIONS
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis. PGCGROWTHCONDITIONS
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: the DNA samples were treated with ultrasound (3-5 pulses of 30 sec at 4°C). After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 20-30 ng PGCGROWTHCONDITIONS
molecule subtype: total RNA, rRNA depleted PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
Overnight cultures of strain JM83 were diluted 1 PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50. PGCGROWTHCONDITIONS
strain: JM83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
treated with: 0.5 μg PGCGROWTHCONDITIONS
treated with: none (untreated control) PGCGROWTHCONDITIONS
Trimethoprim-treated E. coli cells PGCGROWTHCONDITIONS
Untreated E. coli cells PGCGROWTHCONDITIONS
BW25113-pCA24N_arT LB 90 min 1 mM IPTG PGCGROWTHCONDITIONS
BW25113-pCA24N LB 90 min 1 mM IPTG PGCGROWTHCONDITIONS
Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104). PGCGROWTHCONDITIONS
Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice. PGCGROWTHCONDITIONS
Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
overexpression of arT (pCA24N_arT) PGCGROWTHCONDITIONS
overexpression of empty vector (pCA24N) PGCGROWTHCONDITIONS
Strains were grown in LBCm30 at 37°C with shaking at 250 rpm.  Overnight cultures were diluted into fresh LBCm30, grown for 2.5 h, and induced with 1 mM IPTG for 90 min (final OD600 = 1.6). PGCGROWTHCONDITIONS
E. coli 2% NaCl PGCGROWTHCONDITIONS
E. coli 3.5% NaCl, replicate 1 PGCGROWTHCONDITIONS
E. coli 3.5% NaCl, replicate 2 PGCGROWTHCONDITIONS
E. coli 4.5% NaCl PGCGROWTHCONDITIONS
E. coli 5.5% NaCl PGCGROWTHCONDITIONS
E. coli 5% NaCl PGCGROWTHCONDITIONS
E. coli, stressed by NaCl, in presence of glycine betaine PGCGROWTHCONDITIONS
E. coli was grown to exponential phase in glucose minimal medium in the presence of the osmoprotectant glycine beatine with a range of salt concentrations at 2, 3.5 (2 repeats), 4.5, 5 and 5.5% NaCl.  E. coli were inoculated at 104 cfu PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genomic DNA was purified from exponentially growing cells by lysis in lysozyme PGCGROWTHCONDITIONS
growth phase: exponential PGCGROWTHCONDITIONS
growth phase: Exponential PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
The analysis of the data is based on cross validation with datasets generated by Monte-Carlo simulation. The null hypothesis was that the gene expression changes monotonously as a function of NaCl concentration. The existence of a deviation from monotony was tested by F-tests for each gene probe. By comparing the number of probes with the lowest p(F) values for each NaCl concentrations with analogous results generated from Monte-Carlo sampling of the null hypothesis, we show that it is very unlikely that a switch between 4.5 and 5% NaCl could have happened by chance (in fact p<<0.01). PGCGROWTHCONDITIONS
The data were normalised manually in Excel. For each spot, the median of the spot intensity minus the background were considered. Because we wanted to compare different environmental conditions, the cDNA signal in each condition was normalised to that of gDNA with M=ln(cDNA PGCGROWTHCONDITIONS
0.5mg PGCGROWTHCONDITIONS
antibody: anti-DksA rabbit polyclonal antisera PGCGROWTHCONDITIONS
antibody: anti-RNAP b subunit NT63 monoclonal antibodies PGCGROWTHCONDITIONS
antibody: anti-s70 monoclonal antibodies PGCGROWTHCONDITIONS
antibody: None, input DNA PGCGROWTHCONDITIONS
Cells were fixed with 1% formaldehyde for 5min before quenching with ice-cold glycine (100mM). Cells were harvested, washed with ice-cold PBS and flash-frozen in liquid nitrogen. Cell pellets were resuspended in 500 ml of IP buffer (100 mM Tris pH 8, 300mM NaCl, 2% TritonX-100) and sonicated using a Misonix sonicator (S-4000) with a cup horn (431C) set at 60% output, 10 sec ON and 10 sec OFF, for a total sonication time of 16 min. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
DdksA cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg PGCGROWTHCONDITIONS
DksA ChIP DNA from DdksA cells PGCGROWTHCONDITIONS
DksA ChIP DNA from wt cells PGCGROWTHCONDITIONS
DksA_DdksA_untreated PGCGROWTHCONDITIONS
DksA_wt_untreated_rep1 PGCGROWTHCONDITIONS
DksA_wt_untreated_rep2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
genotype: MG1655 DdksA PGCGROWTHCONDITIONS
Input DNA from DdksA cells PGCGROWTHCONDITIONS
Input DNA from starved DdksA cells PGCGROWTHCONDITIONS
Input DNA from starved wt cells PGCGROWTHCONDITIONS
Input DNA from wt cells PGCGROWTHCONDITIONS
None PGCGROWTHCONDITIONS
RNAP ChIP DNA from DdksA cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from starved DdksA cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from starved wt cells PGCGROWTHCONDITIONS
RNAP ChIP DNA from wt cells PGCGROWTHCONDITIONS
RNAP_DdksA_SHX_rep1 PGCGROWTHCONDITIONS
RNAP_DdksA_SHX_rep2 PGCGROWTHCONDITIONS
RNAP_DdksA_untreated_rep1 PGCGROWTHCONDITIONS
RNAP_DdksA_untreated_rep2 PGCGROWTHCONDITIONS
RNAP_wt_SHX_rep1 PGCGROWTHCONDITIONS
RNAP_wt_SHX_rep2 PGCGROWTHCONDITIONS
RNAP_wt_untreated_rep1 PGCGROWTHCONDITIONS
RNAP_wt_untreated_rep2 PGCGROWTHCONDITIONS
s70 ChIP DNA from DdksA cells PGCGROWTHCONDITIONS
s70 ChIP DNA from starved DdksA cells PGCGROWTHCONDITIONS
s70 ChIP DNA from starved wt cells PGCGROWTHCONDITIONS
s70 ChIP DNA from wt cells PGCGROWTHCONDITIONS
s70_DdksA_SHX_rep1 PGCGROWTHCONDITIONS
s70_DdksA_SHX_rep2 PGCGROWTHCONDITIONS
s70_DdksA_untreated_rep1 PGCGROWTHCONDITIONS
s70_DdksA_untreated_rep2 PGCGROWTHCONDITIONS
s70_wt_SHX_rep1 PGCGROWTHCONDITIONS
s70_wt_SHX_rep2 PGCGROWTHCONDITIONS
s70_wt_untreated_rep1 PGCGROWTHCONDITIONS
s70_wt_untreated_rep2 PGCGROWTHCONDITIONS
The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. PGCGROWTHCONDITIONS
treatment: 0.5mg PGCGROWTHCONDITIONS
treatment: None PGCGROWTHCONDITIONS
Wild-types cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg PGCGROWTHCONDITIONS
agent: DPD PGCGROWTHCONDITIONS
agent: DPD and rifampicin PGCGROWTHCONDITIONS
agent: Fe PGCGROWTHCONDITIONS
agent: Fe and rifampicin PGCGROWTHCONDITIONS
chip antibody: anti-myc (Santa Cruz Biotech, sc-28207) PGCGROWTHCONDITIONS
chip antibody: anti-RpoB (Neoclone, WP002) PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Fur with DPD 1 (ChIP-exo) PGCGROWTHCONDITIONS
Fur with DPD 2 (ChIP-exo) PGCGROWTHCONDITIONS
Fur with Fe 1 (ChIP-exo) PGCGROWTHCONDITIONS
Fur with Fe 2 (ChIP-exo) PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Immunoprecipitated DNA PGCGROWTHCONDITIONS
library strategy: ChIP-exo PGCGROWTHCONDITIONS
RpoB with DPD 1 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with DPD 2 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with DPD and rifampicin 1 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with DPD and rifampicin 2 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with Fe 1 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with Fe 2 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with Fe and rifampicin 1 (ChIP-exo) PGCGROWTHCONDITIONS
RpoB with Fe and rifampicin 2 (ChIP-exo) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+ PGCGROWTHCONDITIONS
agent: DPD PGCGROWTHCONDITIONS
agent: Fe PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total RNA isolated from E. coli PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA). PGCGROWTHCONDITIONS
WT with DPD 1 (RNA-seq) PGCGROWTHCONDITIONS
WT with DPD 2 (RNA-seq) PGCGROWTHCONDITIONS
WT with Fe 1 (RNA-seq) PGCGROWTHCONDITIONS
WT with Fe 2 (RNA-seq) PGCGROWTHCONDITIONS
Δfur with DPD 1 (RNA-seq) PGCGROWTHCONDITIONS
Δfur with DPD 2 (RNA-seq) PGCGROWTHCONDITIONS
Δfur with Fe 1 (RNA-seq) PGCGROWTHCONDITIONS
Δfur with Fe 2 (RNA-seq) PGCGROWTHCONDITIONS
Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 10min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 120min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 20min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 40min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM CORM-3 for 60min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 10min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 120min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 20min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 40min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, exposed to 100uM iCORM-3 for 60min PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, prior to CORM-3 addition (t=0) PGCGROWTHCONDITIONS
Batch anaerobically grown cultures in hemA defined medium, prior to iCORM-3 addition PGCGROWTHCONDITIONS
Cells were harvested directly into phenol:ethanol to stabilize RNA and total RNA was purified using Qiagen’s RNeasy Mini Kit, according to the manufacturer's instructions. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 120 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 1_Cy3 120 Cy5 0 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 1_Cy3 60 Cy5 0 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 13_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 120 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 0 Cy5 60 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 120 Cy5 0 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 14_Wild type_CORM-3_biol rep 2_Cy3 60 Cy5 0 PGCGROWTHCONDITIONS
Slide 15_hemA_CORM-3_biol rep 2_Cy3 120 Cy5 0 PGCGROWTHCONDITIONS
Slide 15_hemA_CORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 15_hemA_CORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 15_hemA_CORM-3_biol rep 2_Cy3 60 Cy5 0 PGCGROWTHCONDITIONS
Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 15_Wild type_CORM-3_biol rep 1_Cy3 0 Cy5 60 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 1_Cy3 120 Cy5 0 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 1_Cy3 60 Cy5 0 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 120 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 2_Cy3 0 Cy5 60 PGCGROWTHCONDITIONS
Slide 16_hemA_CORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 120 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 0 Cy5 60 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 17_hemA_CORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 120 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 0 Cy5 60 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 34_hemA_iCORM-3_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 1_Cy3 120 Cy5 0 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 1_Cy3 60 Cy5 0 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 120 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 2_Cy3 0 Cy5 60 PGCGROWTHCONDITIONS
Slide 35_hemA_iCORM-3_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 36_hemA_iCORM-3_biol rep 2_Cy3 120 Cy5 0 PGCGROWTHCONDITIONS
Slide 36_hemA_iCORM-3_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 36_hemA_iCORM-3_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 36_hemA_iCORM-3_biol rep 2_Cy3 60 Cy5 0 PGCGROWTHCONDITIONS
Slide 36_hemA vs. WT t=0_biol rep 1_Cy3 hemA Cy5 WT PGCGROWTHCONDITIONS
Slide 36_hemA vs. WT t=0_biol rep 2_Cy3 hemA Cy5 WT PGCGROWTHCONDITIONS
Slide 36_WT vs. hemA t=0_biol rep 1_Cy3 WT Cy5 hemA PGCGROWTHCONDITIONS
Slide 36_WT vs. hemA t=0_biol rep 2_Cy3 WT Cy5 hemA PGCGROWTHCONDITIONS
strain: hemA strain MG1655 PGCGROWTHCONDITIONS
strain: Wild type strain MG1655 PGCGROWTHCONDITIONS
treatment: exposed to 100uM CORM-3 for 10min PGCGROWTHCONDITIONS
treatment: exposed to 100uM CORM-3 for 120min PGCGROWTHCONDITIONS
treatment: exposed to 100uM CORM-3 for 20min PGCGROWTHCONDITIONS
treatment: exposed to 100uM CORM-3 for 40min PGCGROWTHCONDITIONS
treatment: exposed to 100uM CORM-3 for 60min PGCGROWTHCONDITIONS
treatment: exposed to 100uM iCORM-3 for 10min PGCGROWTHCONDITIONS
treatment: exposed to 100uM iCORM-3 for 120min PGCGROWTHCONDITIONS
treatment: exposed to 100uM iCORM-3 for 20min PGCGROWTHCONDITIONS
treatment: exposed to 100uM iCORM-3 for 40min PGCGROWTHCONDITIONS
treatment: exposed to 100uM iCORM-3 for 60min PGCGROWTHCONDITIONS
treatment: prior to CORM-3 addition (t=0) PGCGROWTHCONDITIONS
treatment: prior to iCORM-3 addition (t=0) PGCGROWTHCONDITIONS
Coverage calculation and normalisation (TRAPL) PGCGROWTHCONDITIONS
Demultiplexing PGCGROWTHCONDITIONS
Escherichia coli MG1655 cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Fastq quality trimming using FastX and a cut-off value of 20 PGCGROWTHCONDITIONS
Fastq to fasta conversion using FastX PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
growth phase: exponential PGCGROWTHCONDITIONS
growth phase: stationary PGCGROWTHCONDITIONS
Hot phenol (Sharma et al. 2010, Bloomberg 1990, EMBO J) PGCGROWTHCONDITIONS
LB 0.4 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
LB 0.4 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
LB 0.4 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
LB 0.4 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
LB 0.4 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
LB 0.4 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
LB 2.0 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
LB 2.0 B1 TEX neg L2 HS2 PGCGROWTHCONDITIONS
LB 2.0 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
LB 2.0 B1 TEX pos L2 HS2 PGCGROWTHCONDITIONS
LB 2.0 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
LB 2.0 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
LB 2.0 B2 TEX neg L2 HS2 PGCGROWTHCONDITIONS
LB 2.0 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
LB 2.0 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
LB 2.0 B2 TEX pos L2 HS2 PGCGROWTHCONDITIONS
M63 0.4 B1 TEX neg L1 GA PGCGROWTHCONDITIONS
M63 0.4 B1 TEX pos L1 GA PGCGROWTHCONDITIONS
M63 0.4 B2 TEX neg L1 HS1 PGCGROWTHCONDITIONS
M63 0.4 B2 TEX neg L1 HS2 PGCGROWTHCONDITIONS
M63 0.4 B2 TEX pos L1 HS1 PGCGROWTHCONDITIONS
M63 0.4 B2 TEX pos L1 HS2 PGCGROWTHCONDITIONS
medium: LB PGCGROWTHCONDITIONS
medium: M63 PGCGROWTHCONDITIONS
Read mapping using segemehl version 0.13 (TRAPL) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were mixed, incubated on ice for 10 min after which cells were collected by centrifugation at 4150 rpm at 4˚C for 10 min.  Cell pellets were snap frozen in an ethanol PGCGROWTHCONDITIONS
Size filtering: discarding reads shorter than 12 nt (TRAPL) PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle PGCGROWTHCONDITIONS
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng PGCGROWTHCONDITIONS
To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4CL_anaerobic PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4CL_anaerobic_1.CEL PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4CL_anaerobic_2.CEL PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4CL_anaerobic_3.CEL PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4Cl_NO3 PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4Cl_NO3_1.CEL PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4Cl_NO3_2.CEL PGCGROWTHCONDITIONS
affyexp_delta-arcA_glucose_NH4Cl_NO3_3.CEL PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4CL_anaerobic PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4CL_anaerobic_1.CEL PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4CL_anaerobic_2.CEL PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4CL_anaerobic_3.CEL PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4Cl_NO3 PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4Cl_NO3_1.CEL PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4Cl_NO3_2.CEL PGCGROWTHCONDITIONS
affyexp_delta-fnr_glucose_NH4Cl_NO3_3.CEL PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4CL_anaerobic PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4CL_anaerobic_1.CEL PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4CL_anaerobic_2.CEL PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4CL_anaerobic_3.CEL PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4Cl_NO3 PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4Cl_NO3_1.CEL PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4Cl_NO3_2.CEL PGCGROWTHCONDITIONS
affyexp_wt_glucose_NH4Cl_NO3_3.CEL PGCGROWTHCONDITIONS
All strains used in this study were E. coli K-12 MG1655 and its derivatives. The deletion mutants (Δfnr and ΔarcA) were constructed by a λ red and FLP-mediated site-specific recombination method. Glycerol stocks of E. coli strains were inoculated into M9 minimal medium containing 0.2% (w PGCGROWTHCONDITIONS
culture condition: anaerobic fermentive condition PGCGROWTHCONDITIONS
culture condition: nitrate respiratory condition PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Raw CEL files were analyzed using robust multi-array average for normalization and calculation of probe intensities. The processed probe signals derived from each microarray were averaged for both the wild type and deletion mutant strains. This was done using the GCRMA package (version 2.13) from Bioconductor in R. PGCGROWTHCONDITIONS
Samples for transcriptome analysis were taken from exponentially growing cells. From the cells treated by RNAprotect Bacteria Reagent (Qiagen), total RNA samples were isolated using RNeasy columns (Qiagen) in accordance with manufacturer’s instruction. PGCGROWTHCONDITIONS
Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug PGCGROWTHCONDITIONS
chip antibody: biotin conjugated anti-c-myc antibody PGCGROWTHCONDITIONS
chip antibody: HRP-conjugated sheep anti-mouse IgG PGCGROWTHCONDITIONS
chip antibody vendor: Amersham Biosciences PGCGROWTHCONDITIONS
chip antibody vendor: Santa Cruz Biotechnology PGCGROWTHCONDITIONS
chip-ArcA_ArcA8myc_glucose_NH4CL_anaerobic_1 PGCGROWTHCONDITIONS
chip-ArcA_ArcA8myc_glucose_NH4CL_anaerobic_2 PGCGROWTHCONDITIONS
chip-ArcA_ArcA8myc_glucose_NH4CL_anaerobic_3 PGCGROWTHCONDITIONS
chip-ArcA_ArcA8myc_glucose_NH4CL_NO3_1 PGCGROWTHCONDITIONS
chip-ArcA_ArcA8myc_glucose_NH4CL_NO3_2 PGCGROWTHCONDITIONS
chip-ArcA_ArcA8myc_glucose_NH4CL_NO3_3 PGCGROWTHCONDITIONS
chip-Fnr_Fnr8myc_glucose_NH4CL_anaerobic_1 PGCGROWTHCONDITIONS
chip-Fnr_Fnr8myc_glucose_NH4CL_anaerobic_2 PGCGROWTHCONDITIONS
chip-Fnr_Fnr8myc_glucose_NH4CL_anaerobic_3 PGCGROWTHCONDITIONS
chip-Fnr_Fnr8myc_glucose_NH4CL_NO3_1 PGCGROWTHCONDITIONS
chip-Fnr_Fnr8myc_glucose_NH4CL_NO3_2 PGCGROWTHCONDITIONS
chip-Fnr_Fnr8myc_glucose_NH4CL_NO3_3 PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of ArcA-8myc and DNA was immunoprecipitated by rabbit serum containing myc antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of ArgR-8myc and DNA was immunoprecipitated by rabbit serum containing myc antibody. PGCGROWTHCONDITIONS
Cross-linked and sonicated chromatin complex of Fnr-8myc and DNA was immunoprecipitated by rabbit serum containing myc antibody. PGCGROWTHCONDITIONS
E. Coli ArcA-8myc ChIP DNA Mock antibody anaerobic PGCGROWTHCONDITIONS
E. Coli ArcA-8myc ChIP DNA Mock antibody NO3 PGCGROWTHCONDITIONS
E. Coli ArcA ChIP DNA anaerobic PGCGROWTHCONDITIONS
E. Coli ArcA ChIP DNA NO3 PGCGROWTHCONDITIONS
E. Coli Fnr-8myc ChIP DNA Mock antibody anaerobic PGCGROWTHCONDITIONS
E. Coli Fnr-8myc ChIP DNA Mock antibody NO3 PGCGROWTHCONDITIONS
E. Coli Fnr ChIP DNA anaerobic PGCGROWTHCONDITIONS
E. Coli Fnr ChIP DNA NO3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP PGCGROWTHCONDITIONS
background strain: BW25113 PGCGROWTHCONDITIONS
CHP files were generated using Affymetrix Expression Control.  Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed. PGCGROWTHCONDITIONS
Cirpofloxacin treated fur mutant sample at T1h, biological rep 1 PGCGROWTHCONDITIONS
Cirpofloxacin treated fur mutant sample at T1h, biological rep 2 PGCGROWTHCONDITIONS
Cirpofloxacin treated WT sample at T1h, biological rep 1 PGCGROWTHCONDITIONS
Cirpofloxacin treated WT sample at T1h, biological rep 2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 and fur mutant strains were cultivated at 37Co in 25 ml of LB medium using Erlenmeyer flasks. 1 ml of OVN culture was transferred to 20 ml of fresh LB medium and cells were incubated in the presence or absence of ciprofloxacin (100 ng PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FUR_CPR_1 PGCGROWTHCONDITIONS
FUR_CPR_2 PGCGROWTHCONDITIONS
FUR_noCPR_1 PGCGROWTHCONDITIONS
FUR_noCPR_2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Non-treated, fur mutant sample at T0, biological rep 1 PGCGROWTHCONDITIONS
Non-treated, fur mutant sample at T0, biological rep 2 PGCGROWTHCONDITIONS
Non-treated, WT control at T0, biological rep 1 PGCGROWTHCONDITIONS
Non-treated, WT control at T0, biological rep 2 PGCGROWTHCONDITIONS
Samples for microarray analyses were taken before ciprofloxacin treatment (t0) and then at 1 hour post-treatment (t1). Cell concentration was adjusted to 109 cells PGCGROWTHCONDITIONS
We compared the microarray-determined mRNA profiles (Affymetrix E. coli Genome 2.0 Array) of Δfur and WT genotypes in response to ciprofloxacin treatment (100 ng PGCGROWTHCONDITIONS
WT_CPR_1 PGCGROWTHCONDITIONS
WT_CPR_2 PGCGROWTHCONDITIONS
WT_noCPR_1 PGCGROWTHCONDITIONS
WT_noCPR_2 PGCGROWTHCONDITIONS
Cells were grown in the minimal media, modified M63. The final cell concentrations were controlled ~ 10^8 cells PGCGROWTHCONDITIONS
condition: histidine depleted PGCGROWTHCONDITIONS
condition: histidine supplied, 1 mM PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). The log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record. PGCGROWTHCONDITIONS
OSU11, histidine depleted, >10 hrs PGCGROWTHCONDITIONS
OSU11, histidine depleted, >10 hrs, rep 1 PGCGROWTHCONDITIONS
OSU11, histidine depleted, >10 hrs, rep 2 PGCGROWTHCONDITIONS
OSU11, histidine depleted, >10 hrs, rep 3 PGCGROWTHCONDITIONS
OSU11, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU11, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU11, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU11, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU11, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU11, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU11, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU11, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU11, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU11, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU11, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU11, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, >10 hrs PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, >10 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, >10 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, >10 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisA, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisA, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisA, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisA, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisA, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, >10 hrs PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, >10 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, >10 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, >10 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisB, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisB, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisB, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisB, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisB, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, >10 hrs PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, >10 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, >10 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, >10 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisC, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisC, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisC, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisC, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisC, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisD, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisD, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisD, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisD, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisD, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, >10 hrs PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, >10 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, >10 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, >10 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisF, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisF, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisF, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisF, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisF, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisG, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisG, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisG, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisG, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisG, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, >10 hrs PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, >10 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, >10 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, >10 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 10 min PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 10 min, rep 1 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 10 min, rep 2 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 10 min, rep 3 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 2 hrs PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 2 hrs, rep 1 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 2 hrs, rep 2 PGCGROWTHCONDITIONS
OSU12-hisI, histidine depleted, 2 hrs, rep 3 PGCGROWTHCONDITIONS
OSU12-hisI, histidine supplied, 1 mM PGCGROWTHCONDITIONS
OSU12-hisI, histidine supplied, 1 mM, rep 1 PGCGROWTHCONDITIONS
OSU12-hisI, histidine supplied, 1 mM, rep 2 PGCGROWTHCONDITIONS
OSU12-hisI, histidine supplied, 1 mM, rep 3 PGCGROWTHCONDITIONS
strain: DH1 ΔhisA::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔhisB::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔhisC::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔhisD::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔhisF::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔhisG::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔhisI::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
strain: DH1 ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5 PGCGROWTHCONDITIONS
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions. PGCGROWTHCONDITIONS
After 5 h of NP-TiO2 (or mQ water for the control) exposure, cells were incubated for 5 min with two volumes of RNAprotect Bacteria Reagent (Qiagen SAS, France) at room temperature. Cells were then pelleted by centrifugation (7,000 g, 10 min) and the pellet stored at -80°C. PGCGROWTHCONDITIONS
Cell exposure to NP-TiO2 was conducted in 50 ml of sterile Milli-Q water supplemented with 10 mM NaCl. Briefly, 500 µl of the E. coli bacterial suspension and 500 µl of the NP-TiO2 stock suspension (or mQ water for the control) were prepared as previously described and then added to the NaCl solution to obtain final concentrations of 10E7 cells PGCGROWTHCONDITIONS
Ecoli_control_5h_rep1 PGCGROWTHCONDITIONS
Ecoli_control_5h_rep2 PGCGROWTHCONDITIONS
Ecoli_control_5h_rep3 PGCGROWTHCONDITIONS
Ecoli_control_5h_rep4 PGCGROWTHCONDITIONS
E.coli, control culture, 5h in 10 mM NaCl, replicate 1 PGCGROWTHCONDITIONS
E.coli, control culture, 5h in 10 mM NaCl, replicate 2 PGCGROWTHCONDITIONS
E.coli, control culture, 5h in 10 mM NaCl, replicate 3 PGCGROWTHCONDITIONS
E.coli, control culture, 5h in 10 mM NaCl, replicate 4 PGCGROWTHCONDITIONS
Ecoli_NP-TiO2_5h_rep1 PGCGROWTHCONDITIONS
Ecoli_NP-TiO2_5h_rep2 PGCGROWTHCONDITIONS
Ecoli_NP-TiO2_5h_rep3 PGCGROWTHCONDITIONS
Ecoli_NP-TiO2_5h_rep4 PGCGROWTHCONDITIONS
E.coli,  NP-TiO2 exposed culture, 5h in 10 mM NaCl 100mg PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Image analysis was performed with GenePix Pro 7 software (Molecular Device), background was defined with the “Local features background median” method. Quantile normalization was applied on the total number of spots in R (version 2.11.1) with the LIMMA software package. Spots corresponding to the E. coli MG1655 K12 species were extracted. PGCGROWTHCONDITIONS
incubation condition: In the dark, 5h, 20°C, 150 rpm PGCGROWTHCONDITIONS
incubation medium: 10 mM NaCl PGCGROWTHCONDITIONS
incubation medium: 10 mM NaCl + 100mg PGCGROWTHCONDITIONS
Total RNA was extracted from cells with the UltraClean Microbial RNA isolation kit (MO BIO, CA, USA). After extraction, contaminating DNA was digested with DNAse I (Sigma Aldrich) and total RNA was purified by phenol PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 100 μg PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 10 μg PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours without treatment. PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 100 μg PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 10 μg PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours without treatment PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 100 μg PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 10 μg PGCGROWTHCONDITIONS
E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours without treatment PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene selection was done using the False Discovery Rate (FDR) correction procedure for adjusting genes with p-value smaller than 0.05 and Fold Change greater than 2. PGCGROWTHCONDITIONS
genotype: ∆mazEF PGCGROWTHCONDITIONS
genotype: ∆mazEFlexA3 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
∆mazEF 0 μg PGCGROWTHCONDITIONS
∆mazEF 100 μg PGCGROWTHCONDITIONS
∆mazEF 10 μg PGCGROWTHCONDITIONS
∆mazEFlexA3 0 μg PGCGROWTHCONDITIONS
∆mazEFlexA3 100 μg PGCGROWTHCONDITIONS
∆mazEFlexA3 10 μg PGCGROWTHCONDITIONS
RMA normalization was performed on CELL files using the Partek Genomic Suite 6.5. Additional statistical analysis was carried out using the Spotfire software package (Somerville, MA, USA) and custom Matlab (R2010B) routines. PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 100 μg PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours with 10 μg PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ in mid log phase incubated at 37ºC for 4 hours without treatment. PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 100 μg PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours with 10 μg PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ ∆mazEF in mid log phase incubated at 37ºC for 4 hours without treatment PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 100 μg PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours with 10 μg PGCGROWTHCONDITIONS
sample type: E. coli strain MC4100relA+ ∆mazEFlexA3 in mid log phase incubated at 37ºC for 4 hours without treatment PGCGROWTHCONDITIONS
treatment: 0 μg PGCGROWTHCONDITIONS
treatment: 100 μg PGCGROWTHCONDITIONS
treatment: 10 μg PGCGROWTHCONDITIONS
We extracted RNA using RNAprotect Bacteria reagent (Qiagen) and RNeasy Mini Kit (Qiagen) combined with RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
We grew cells in 10 ml M9 minimal medium to OD600=0.5-0.6. Then, we divided each culture into 500µl aliquots to which we added the appropriate concentration of NA. PGCGROWTHCONDITIONS
We incubated each aliquot at 37ºC for 4 hours with NA PGCGROWTHCONDITIONS
WT 0 μg PGCGROWTHCONDITIONS
WT 100 μg PGCGROWTHCONDITIONS
WT 10 μg PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T0 RNA rep 1 PGCGROWTHCONDITIONS
Mutant (EP61) T0 RNA rep 2 PGCGROWTHCONDITIONS
Mutant (EP61) T0 RP rep 1 PGCGROWTHCONDITIONS
Mutant (EP61) T0 RP rep 2 PGCGROWTHCONDITIONS
Mutant (EP61) T1 RNA rep 1 PGCGROWTHCONDITIONS
Mutant (EP61) T1 RNA rep 2 PGCGROWTHCONDITIONS
Mutant (EP61) T1 RP rep 1 PGCGROWTHCONDITIONS
Mutant (EP61) T1 RP rep 2 PGCGROWTHCONDITIONS
Mutant (EP61) T2 RNA rep 1 PGCGROWTHCONDITIONS
Mutant (EP61) T2 RNA rep 2 PGCGROWTHCONDITIONS
Mutant (EP61) T2 RP rep 1 PGCGROWTHCONDITIONS
Mutant (EP61) T2 RP rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T0 RNA rep 2 PGCGROWTHCONDITIONS
Wild-type (MG1655) T0 RP rep 1 PGCGROWTHCONDITIONS
Wild-type (MG1655) T0 RP rep 2 PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RNA rep 1 PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RNA rep 2 PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RP rep 1 PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RP rep 2 PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RNA rep 1 PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RNA rep 2 PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RP rep 1 PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RP rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.7 PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 degrees C in gas-sparged Roux bottles to mid-log phase. PGCGROWTHCONDITIONS
Culture samples were transferred directly into an ice-cold ethanol PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v1, U00096.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Parkhomchuk et al. 2009, Nucleic Acids Res 37: e123. Briefly, ribosome-depleted RNA was fragmented and used as template for cDNA synhtesis. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand. cDNAs were size-selected and ligated to sequencing adapters followed by dUTP cleavage to generate adapter-ligated single-stranded cDNAs. PGCGROWTHCONDITIONS
Mutant (RL2325) RNA-seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were mapped to the E. coli K-12 MG1655 genome (GenBank ID U00096.2) using short oligonucleotide alignment program (SOAP) PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
strain: RL2325 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files normalized to reads per million per position.  Those designated \minus\ cover the minus strand of the genome; those with designated \plus\ cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) RNA-seq PGCGROWTHCONDITIONS
Bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the reference genome were converted to wiggle files. The position of each alignment was mapped to the 3' end of the nascent transcript. PGCGROWTHCONDITIONS
Cell culture was rapidly filtered in 250 mL increments at 37 °C over 0.22 μm nitrocellulose filters (GE) and frozen in liquid nitrogen to simultaneously halt all transcriptional progress. Frozen cells (100 μg) were pulverized on a Qiagen TissueLyser II mixer mill 6 times at 15 Hz for 3 min in the presence of 500 μL frozen lysis buffer (20 mM Tris pH 8, 0.4% Triton X-100, 0.1% NP-40, 100 mM NH4Cl, 50 U PGCGROWTHCONDITIONS
Ecoli_WT_RNAseq PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each sample, 500 mL liquid cultures were grown in 2.8 L flasks with shaking (180 rpm) at 37 °C from an OD (600 nm) 0.05 to OD 0.45 ± 0.05. Cells were grown in MOPS EZ rich defined medium with 0.2% glucose (Teknova). PGCGROWTHCONDITIONS
Genome_build: E. coli: NC_000913 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
media: MOPS EZ Rich Defined Media PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The full library construction protocol was described in detail previously (Churchman et al., Nature 2011). Purified total RNA was fragmented and dephosphorylated with T4 PNK, and then ligated to a 5' adenylated DNA oligo to generate RNA ranging from 30-100 nt. The RNA was reverse transcribed, and the single-stranded DNA circularized and PCR amplified. PGCGROWTHCONDITIONS
Trimmed reads were aligned using Bowtie v0.12.7 against the reference genome using parameters -a -v 3 -m 1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
EvgSc_1 PGCGROWTHCONDITIONS
EvgSc_2 PGCGROWTHCONDITIONS
EvgSc mutant rep 1 PGCGROWTHCONDITIONS
EvgSc mutant rep 2 PGCGROWTHCONDITIONS
EvgSc_ompR_1 PGCGROWTHCONDITIONS
EvgSc_ompR_2 PGCGROWTHCONDITIONS
EvgSc ompR double mutant rep 1 PGCGROWTHCONDITIONS
EvgSc ompR double mutant rep 2 PGCGROWTHCONDITIONS
genotype: EvgSc KO PGCGROWTHCONDITIONS
genotype: EvgSc ompR KO PGCGROWTHCONDITIONS
genotype: ompR KO PGCGROWTHCONDITIONS
genotype: Wild Type PGCGROWTHCONDITIONS
LB media PGCGROWTHCONDITIONS
ompR_1 PGCGROWTHCONDITIONS
ompR_2 PGCGROWTHCONDITIONS
ompR mutant rep 1 PGCGROWTHCONDITIONS
ompR mutant rep 2 PGCGROWTHCONDITIONS
RNA was extracted using RNAeasy columns (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08). PGCGROWTHCONDITIONS
wild type rep 1 PGCGROWTHCONDITIONS
wild type rep 2 PGCGROWTHCONDITIONS
WT_1 PGCGROWTHCONDITIONS
WT_2 PGCGROWTHCONDITIONS
Automatic extractor in Verigene system of genomic DNA PGCGROWTHCONDITIONS
Blood culture PGCGROWTHCONDITIONS
Blood culture bottle PGCGROWTHCONDITIONS
culture system: BACTEC PGCGROWTHCONDITIONS
Direct testing of culture broth (Standard) or after centrifugation of culture broth (Supernatant) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gram status: Gram-negative PGCGROWTHCONDITIONS
Sample 79 PGCGROWTHCONDITIONS
Scatter signal intensity after illumination at 150 ms exposure without normalization, without transformation. The non-normalized signals form the basis of conclusions in the accompanying manuscript. PGCGROWTHCONDITIONS
source: Peripheral blood PGCGROWTHCONDITIONS
treatment: Supernatant PGCGROWTHCONDITIONS
Cells were grown at 30°C in LB medium to an OD600 of 0.55-0.6 PGCGROWTHCONDITIONS
culture denity: OD600=0.55-0.6 culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
LOWESS normalized, background subtracted data obtained from signals. Agilent GeneSpring GX 7.3 was used. PGCGROWTHCONDITIONS
pFlag-only control PGCGROWTHCONDITIONS
RhIB wild type PGCGROWTHCONDITIONS
RhlBP238L mutant PGCGROWTHCONDITIONS
RhlBP238L vs flag only 1 PGCGROWTHCONDITIONS
RhlBP238L vs flag only 2 PGCGROWTHCONDITIONS
RhlBP238L vs flag only 3 PGCGROWTHCONDITIONS
RhlBwt vs flag only 1 PGCGROWTHCONDITIONS
RhlBwt vs flag only 2 PGCGROWTHCONDITIONS
RhlBwt vs flag only 3 PGCGROWTHCONDITIONS
strain: BL21 (DE3) rne131 DrhlB PGCGROWTHCONDITIONS
Total RNA was isolated according to the RNeasy Mini Kit (QIAGEN) manufacturer's protocol. PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vitro PGCGROWTHCONDITIONS
analysis: in vivo PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: n PGCGROWTHCONDITIONS
genotype: rne-3071 (ts) PGCGROWTHCONDITIONS
genotype: rne wild-type PGCGROWTHCONDITIONS
genotype: rng mutant PGCGROWTHCONDITIONS
genotype: rng wild-type PGCGROWTHCONDITIONS
incubation time: 0 min PGCGROWTHCONDITIONS
incubation time: 10 min PGCGROWTHCONDITIONS
incubation time: n PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rne-3071 ts PGCGROWTHCONDITIONS
rne wild-type PGCGROWTHCONDITIONS
rng mutant PGCGROWTHCONDITIONS
rng wild-type PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
strain: GM11 PGCGROWTHCONDITIONS
strain: MC1061 PGCGROWTHCONDITIONS
strain: N3431 PGCGROWTHCONDITIONS
strain: N3433 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
T170V 0 min PGCGROWTHCONDITIONS
T170V 10 min PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: rpoS PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
growth phase: Log phase OD 0.4 PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rpoS_N_strv PGCGROWTHCONDITIONS
rpoS_N_strv_TEX PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Carbon starvation PGCGROWTHCONDITIONS
treatment: log phase sample PGCGROWTHCONDITIONS
treatment: Nitrogen starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_glucose_log PGCGROWTHCONDITIONS
WT_glucose_log_TEX PGCGROWTHCONDITIONS
WT_glucose_stat PGCGROWTHCONDITIONS
WT_glucose_stat_TEX PGCGROWTHCONDITIONS
WT_N_strv PGCGROWTHCONDITIONS
WT_N_strv_TEX PGCGROWTHCONDITIONS
10 mM of sodium phosphate and formaldehyde to a final concentration of 1% were then added. After 10min of incubation at room temperature, the samples were incubated 30 min in ice PGCGROWTHCONDITIONS
bacterial cell culture PGCGROWTHCONDITIONS
chip antibody: anti-Flag (Sigma) PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Cross-linked cells were harvested and washed two times with ice-cold PBS. Cells were resuspended in 450μl of TES buffer (50mM Tris-HCl pH 7.5, 150mM NaCl) and 20μl of lysis solution (13.6mg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Reference genome used: Escherichia coli K12 MG1655, version: iGenome PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
genotype: ΔbolA PGCGROWTHCONDITIONS
Library construction was performed by processing in vitro samples to generate a library of short inserts (the DNA Colonies Template Library) by Fasteris SA, Switzerland PGCGROWTHCONDITIONS
Mapping was performed using BWA tool (version 0.5.9) against the reference genome PGCGROWTHCONDITIONS
Peak detection and count of coverage were done using SEQMONK version 0.21.0 by Fasteris SA PGCGROWTHCONDITIONS
Reference genome used: Escherichia coli K12 MG1655, version: iGenome PGCGROWTHCONDITIONS
strain: no tag PGCGROWTHCONDITIONS
strain: wt 3xflag strain PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt file file with raw and normalized counts of coverage PGCGROWTHCONDITIONS
The ΔbolA and wt 3xflag strains were used to perform ChIP-seq experiments. Overnight cultures were diluted 1 PGCGROWTHCONDITIONS
wild type PGCGROWTHCONDITIONS
ΔbolA PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
molecule subtype: ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
mRNA-seq MicL-S t0 PGCGROWTHCONDITIONS
mRNA-seq MicL-S t10 PGCGROWTHCONDITIONS
mRNA-seq MicL-S t20 PGCGROWTHCONDITIONS
mRNA-seq MicL-S t4 PGCGROWTHCONDITIONS
mRNA-seq MicL t0 PGCGROWTHCONDITIONS
mRNA-seq MicL t10 PGCGROWTHCONDITIONS
mRNA-seq MicL t20 PGCGROWTHCONDITIONS
mRNA-seq MicL t4 PGCGROWTHCONDITIONS
mRNA-seq Vector t0 PGCGROWTHCONDITIONS
mRNA-seq Vector t20 PGCGROWTHCONDITIONS
mRNA-seq WT t10 PGCGROWTHCONDITIONS
mRNA-seq WT t4 PGCGROWTHCONDITIONS
plasmid: empty vector PGCGROWTHCONDITIONS
plasmid: pMicL PGCGROWTHCONDITIONS
plasmid: pMicL-S PGCGROWTHCONDITIONS
ribosome profiling in rich defined media PGCGROWTHCONDITIONS
ribosome profiling MicL t0 PGCGROWTHCONDITIONS
ribosome profiling MicL t20 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
biological replicate: 318 PGCGROWTHCONDITIONS
biological replicate: 320 PGCGROWTHCONDITIONS
biological replicate: 327 PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
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
GLBRCE1, ACSH, Exp PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Exp_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Exp_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Exp_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, ACSH, Stat1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat1_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat1_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat1_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, ACSH, Stat2 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat2_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat2_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat2_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, ACSH, Trans PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Trans_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Trans_rep318_2 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Trans_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Trans_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH, Exp PGCGROWTHCONDITIONS
GLBRCE1_SynH_Exp_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Exp_rep318_2 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Exp_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Exp_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH_LT, Exp PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Exp_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Exp_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Exp_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH_LT, Stat1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Stat1_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Stat1_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Stat1_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH_LT, Stat2 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Stat2_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Stat2_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Stat2_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH_LT, Trans PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Trans_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Trans_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_LT_Trans_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH, Stat1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Stat1_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Stat1_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Stat1_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH, Stat2 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Stat2_rep327_1 PGCGROWTHCONDITIONS
GLBRCE1, SynH, Trans PGCGROWTHCONDITIONS
GLBRCE1_SynH_Trans_rep318_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Trans_rep320_1 PGCGROWTHCONDITIONS
GLBRCE1_SynH_Trans_rep327_1 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
growth phase: Stat2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
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. PGCGROWTHCONDITIONS
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
strain: GLBRCE1 PGCGROWTHCONDITIONS
technical replicate: 1 PGCGROWTHCONDITIONS
technical replicate: 2 PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol PGCGROWTHCONDITIONS
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. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1_pBBR PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Exp PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Stat PGCGROWTHCONDITIONS
GLBRCE1_ACSH_Trans PGCGROWTHCONDITIONS
GLBRCE1_pBBR_ACSH_Exp PGCGROWTHCONDITIONS
GLBRCE1_pBBR_ACSH_Stat PGCGROWTHCONDITIONS
GLBRCE1_pBBR_ACSH_Trans PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
growth phase: Stat PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
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. PGCGROWTHCONDITIONS
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
strain: GLBRCE1 PGCGROWTHCONDITIONS
strain: GLBRCE1_pBBR PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
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
growth phase: log phase PGCGROWTHCONDITIONS
growth phase: stat 1 PGCGROWTHCONDITIONS
growth phase: stat 2 PGCGROWTHCONDITIONS
growth phase: transition PGCGROWTHCONDITIONS
LIMS477_S1_T10 PGCGROWTHCONDITIONS
LIMS477_S1_T3 PGCGROWTHCONDITIONS
LIMS477_S1_T6 PGCGROWTHCONDITIONS
LIMS477_S2_T4 PGCGROWTHCONDITIONS
LIMS477_S2_T6 PGCGROWTHCONDITIONS
LIMS477_S2_T8 PGCGROWTHCONDITIONS
LIMS477_S3_T11 PGCGROWTHCONDITIONS
LIMS477_S3_T3 PGCGROWTHCONDITIONS
LIMS477_S3_T6 PGCGROWTHCONDITIONS
LIMS477_S5_T4 PGCGROWTHCONDITIONS
LIMS477_S5_T6 PGCGROWTHCONDITIONS
LIMS477_S5_T8 PGCGROWTHCONDITIONS
LIMS484_S1_T3 PGCGROWTHCONDITIONS
LIMS484_S1_T6 PGCGROWTHCONDITIONS
LIMS484_S1_T8 PGCGROWTHCONDITIONS
LIMS484_S2_T2 PGCGROWTHCONDITIONS
LIMS484_S2_T6 PGCGROWTHCONDITIONS
LIMS484_S2_T8 PGCGROWTHCONDITIONS
LIMS484_S5_T2 PGCGROWTHCONDITIONS
LIMS484_S5_T6 PGCGROWTHCONDITIONS
LIMS484_S5_T8 PGCGROWTHCONDITIONS
LIMS484_S6_T4 PGCGROWTHCONDITIONS
LIMS484_S6_T6 PGCGROWTHCONDITIONS
LIMS484_S6_T8 PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
medium: SynH + LTs PGCGROWTHCONDITIONS
medium: SynH w PGCGROWTHCONDITIONS
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. PGCGROWTHCONDITIONS
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
strain: GLBRCE1 PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Fermentations were carried out in 3L bioreactors (Applikon Biotechnology) containing 2.45L of ACSH, SynH, SynH+LT, or SynH + Acid PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
growth phase: Exp1 PGCGROWTHCONDITIONS
growth phase: Exp2 PGCGROWTHCONDITIONS
growth phase: Exp3 PGCGROWTHCONDITIONS
growth phase: Stat PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
growth phase: Stat2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
medium: SynH_Acids_Amides PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
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. PGCGROWTHCONDITIONS
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
strain: GLBRCE1 PGCGROWTHCONDITIONS
X515_V1_T4_424287A03 PGCGROWTHCONDITIONS
X515_V1_T4_475655A02 PGCGROWTHCONDITIONS
X515_V1_T6_475649A04s PGCGROWTHCONDITIONS
X515_V1_T7_475654A02 PGCGROWTHCONDITIONS
X515_V1_T8_475585A04 PGCGROWTHCONDITIONS
X515_V2_T4_424219A04 PGCGROWTHCONDITIONS
X515_V2_T4_475655A03 PGCGROWTHCONDITIONS
X515_V2_T6_475644A04 PGCGROWTHCONDITIONS
X515_V2_T7_475649A01 PGCGROWTHCONDITIONS
X515_V2_T8_424219A01s PGCGROWTHCONDITIONS
X515_V3_T4_475585A02s PGCGROWTHCONDITIONS
X515_V3_T6_424221A04 PGCGROWTHCONDITIONS
X515_V3_T7_475649A02 PGCGROWTHCONDITIONS
X515_V3_T8_475641A04 PGCGROWTHCONDITIONS
X515_V4_T4_475585A03 PGCGROWTHCONDITIONS
X515_V4_T4_475644A01 PGCGROWTHCONDITIONS
X515_V4_T6_424221A03 PGCGROWTHCONDITIONS
X515_V4_T7_424287A04 PGCGROWTHCONDITIONS
X515_V4_T8_475655A04 PGCGROWTHCONDITIONS
X520_V1_T4_424221A01 PGCGROWTHCONDITIONS
X520_V1_T6_475649A03 PGCGROWTHCONDITIONS
X520_V1_T7_475655A01 PGCGROWTHCONDITIONS
X520_V1_T8_475641A01 PGCGROWTHCONDITIONS
X520_V2_T3_424221A02 PGCGROWTHCONDITIONS
X520_V2_T4_475641A03 PGCGROWTHCONDITIONS
X520_V2_T6_424287A02 PGCGROWTHCONDITIONS
X520_V2_T7_475654A01 PGCGROWTHCONDITIONS
X520_V2_T8_424219A02 PGCGROWTHCONDITIONS
X520_V3_T4_475654A04 PGCGROWTHCONDITIONS
X520_V3_T6_475641A02 PGCGROWTHCONDITIONS
X520_V3_T7_475644A02s PGCGROWTHCONDITIONS
X520_V3_T8_424219A03 PGCGROWTHCONDITIONS
X520_V4_T4_475654A03 PGCGROWTHCONDITIONS
X520_V4_T6_424287A01 PGCGROWTHCONDITIONS
X520_V4_T7_475644A03 PGCGROWTHCONDITIONS
X520_V4_T8_475585A01 PGCGROWTHCONDITIONS
Each strain was inoculated from the frozen stock into 10 mL of M9 medium for preculture. Five-microliter aliquots of preculture medium cells were inoculated into the fresh minimal media, M9 with 5%(v PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Evolved strain A, time point 1 PGCGROWTHCONDITIONS
Evolved strain A, time point 2 PGCGROWTHCONDITIONS
Evolved strain A, time point 3 PGCGROWTHCONDITIONS
Evolved strain A, time point 4 PGCGROWTHCONDITIONS
Evolved strain A, time point 5 PGCGROWTHCONDITIONS
Evolved strain B, time point 1 PGCGROWTHCONDITIONS
Evolved strain B, time point 2 PGCGROWTHCONDITIONS
Evolved strain B, time point 3 PGCGROWTHCONDITIONS
Evolved strain B, time point 4 PGCGROWTHCONDITIONS
Evolved strain B, time point 5 PGCGROWTHCONDITIONS
Evolved strain C, time point 1 PGCGROWTHCONDITIONS
Evolved strain C, time point 2 PGCGROWTHCONDITIONS
Evolved strain C, time point 3 PGCGROWTHCONDITIONS
Evolved strain C, time point 4 PGCGROWTHCONDITIONS
Evolved strain C, time point 5 PGCGROWTHCONDITIONS
Evolved strain D, time point 1 PGCGROWTHCONDITIONS
Evolved strain D, time point 2 PGCGROWTHCONDITIONS
Evolved strain D, time point 3 PGCGROWTHCONDITIONS
Evolved strain D, time point 4 PGCGROWTHCONDITIONS
Evolved strain D, time point 5 PGCGROWTHCONDITIONS
Evolved strain E, time point 1 PGCGROWTHCONDITIONS
Evolved strain E, time point 2 PGCGROWTHCONDITIONS
Evolved strain E, time point 3 PGCGROWTHCONDITIONS
Evolved strain E, time point 4 PGCGROWTHCONDITIONS
Evolved strain E, time point 5 PGCGROWTHCONDITIONS
Evolved strain F, time point 1 PGCGROWTHCONDITIONS
Evolved strain F, time point 2 PGCGROWTHCONDITIONS
Evolved strain F, time point 3 PGCGROWTHCONDITIONS
Evolved strain F, time point 4 PGCGROWTHCONDITIONS
Evolved strain F, time point 5 PGCGROWTHCONDITIONS
Log10 mRNA concentration (pM) data are provided as a supplementary file. Expression levels were normalized using the quantile normalization method (Bolstad et al., 2003). PGCGROWTHCONDITIONS
Parent strain of experimental evolution PGCGROWTHCONDITIONS
Parent strain of experimental evolution as adaptive evolved E. coli W3110 strain to M9 synthetic medium without ethanol stress PGCGROWTHCONDITIONS
platform_id_id design: EcFS_1 PGCGROWTHCONDITIONS
platform_id_id design: EcFS_2 PGCGROWTHCONDITIONS
platform_id_id design: EcFS_3 PGCGROWTHCONDITIONS
Strain A of experimental evolution under ethanol stress in 1224 hours. PGCGROWTHCONDITIONS
Strain A of experimental evolution under ethanol stress in 1824 hours. PGCGROWTHCONDITIONS
Strain A of experimental evolution under ethanol stress in 2496 hours. PGCGROWTHCONDITIONS
Strain A of experimental evolution under ethanol stress in 384 hours. PGCGROWTHCONDITIONS
Strain A of experimental evolution under ethanol stress in 744 hours. PGCGROWTHCONDITIONS
strain B of experimental evolution under ethanol stress in 1224 hours. PGCGROWTHCONDITIONS
strain B of experimental evolution under ethanol stress in 1824 hours. PGCGROWTHCONDITIONS
strain B of experimental evolution under ethanol stress in 2496 hours. PGCGROWTHCONDITIONS
strain B of experimental evolution under ethanol stress in 384 hours. PGCGROWTHCONDITIONS
strain B of experimental evolution under ethanol stress in 744 hours. PGCGROWTHCONDITIONS
strain C of experimental evolution under ethanol stress in 1224 hours. PGCGROWTHCONDITIONS
strain C of experimental evolution under ethanol stress in 1824 hours. PGCGROWTHCONDITIONS
strain C of experimental evolution under ethanol stress in 2496 hours. PGCGROWTHCONDITIONS
strain C of experimental evolution under ethanol stress in 384 hours. PGCGROWTHCONDITIONS
strain C of experimental evolution under ethanol stress in 744 hours. PGCGROWTHCONDITIONS
strain D of experimental evolution under ethanol stress in 1224 hours. PGCGROWTHCONDITIONS
strain D of experimental evolution under ethanol stress in 1824 hours. PGCGROWTHCONDITIONS
strain D of experimental evolution under ethanol stress in 2496 hours. PGCGROWTHCONDITIONS
strain D of experimental evolution under ethanol stress in 384 hours. PGCGROWTHCONDITIONS
strain D of experimental evolution under ethanol stress in 744 hours. PGCGROWTHCONDITIONS
strain E of experimental evolution under ethanol stress in 1224 hours. PGCGROWTHCONDITIONS
strain E of experimental evolution under ethanol stress in 1824 hours. PGCGROWTHCONDITIONS
strain E of experimental evolution under ethanol stress in 2496 hours. PGCGROWTHCONDITIONS
strain E of experimental evolution under ethanol stress in 384 hours. PGCGROWTHCONDITIONS
strain E of experimental evolution under ethanol stress in 744 hours. PGCGROWTHCONDITIONS
strain F of experimental evolution under ethanol stress in 1224 hours. PGCGROWTHCONDITIONS
strain F of experimental evolution under ethanol stress in 1824 hours. PGCGROWTHCONDITIONS
strain F of experimental evolution under ethanol stress in 2496 hours. PGCGROWTHCONDITIONS
strain F of experimental evolution under ethanol stress in 384 hours. PGCGROWTHCONDITIONS
strain F of experimental evolution under ethanol stress in 744 hours. PGCGROWTHCONDITIONS
The cells were collected by centrifugation at 8,000 × g for 5 min at 25°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
To obtain the absolute expression levels of genes from microarray raw data, we used the Finite Hybridization model (Furusawa et al, 2009; Ono et al, 2008). PGCGROWTHCONDITIONS
Total RNA was isolated and purified from cells using an RNeasy mini kit with on-column DNA digestion. PGCGROWTHCONDITIONS
ACSH_Exp_CIYS PGCGROWTHCONDITIONS
ACSH_Exp_CNFT PGCGROWTHCONDITIONS
ACSH_Stat1_CNFW PGCGROWTHCONDITIONS
ACSH_Stat1_CNGG PGCGROWTHCONDITIONS
ACSH_Trans_CIYT PGCGROWTHCONDITIONS
ACSH_Trans_CNFU PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
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 '--nofw' 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
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
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
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
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Exp_BXHU PGCGROWTHCONDITIONS
SynH_Exp_CBYS PGCGROWTHCONDITIONS
SynH_LT_Exp_BXNX PGCGROWTHCONDITIONS
SynH_LT_Exp_CBYU PGCGROWTHCONDITIONS
SynH_LT_Exp_CCOG PGCGROWTHCONDITIONS
SynH_LT_Stat1_BXNB PGCGROWTHCONDITIONS
SynH_LT_Stat1_BXNZ PGCGROWTHCONDITIONS
SynH_LT_Stat1_CHBW PGCGROWTHCONDITIONS
SynH_LT_Trans_BXNC PGCGROWTHCONDITIONS
SynH_LT_Trans_BXXC PGCGROWTHCONDITIONS
SynH_LT_Trans_CBYW PGCGROWTHCONDITIONS
SynH_Stat1_CBYN PGCGROWTHCONDITIONS
SynH_Stat1_CUOC PGCGROWTHCONDITIONS
SynH_Trans_CUNZ PGCGROWTHCONDITIONS
SynH_Trans_CUOB PGCGROWTHCONDITIONS
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' 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
BW25113 HEPES-glu 30 min 4.5% deoxycholate PGCGROWTHCONDITIONS
BW25113 with deoxycholate stress PGCGROWTHCONDITIONS
BW25113 ΔmqsRA HEPES-glu 30 min 4.5% deoxycholate PGCGROWTHCONDITIONS
BW25113 ΔmqsRA with deoxycholate stress PGCGROWTHCONDITIONS
Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104). PGCGROWTHCONDITIONS
Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice. PGCGROWTHCONDITIONS
Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Strains were grown in LB at 37°C with shaking at 250 rpm.  16 h overnight cultures were diluted to OD600 = 0.05 in HEPES-glucose (0.4%), grown to OD600 ~ 0.6, and exposed to 4.5% deoxycholate for 30 min. PGCGROWTHCONDITIONS
0.2 ppm deoxynivalenol PGCGROWTHCONDITIONS
0.2 ppm nivalenol PGCGROWTHCONDITIONS
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples. PGCGROWTHCONDITIONS
2 ppm deoxynivalenol PGCGROWTHCONDITIONS
2 ppm nivalenol PGCGROWTHCONDITIONS
acetonitrile PGCGROWTHCONDITIONS
Bacterial culture with 0.2 ppm deoxynivalenol PGCGROWTHCONDITIONS
Bacterial culture with 0.2 ppm nivalenol PGCGROWTHCONDITIONS
Bacterial culture with 2 ppm deoxynivalenol PGCGROWTHCONDITIONS
Bacterial culture with 2 ppm nivalenol PGCGROWTHCONDITIONS
Bacterial culture with acetonitrile PGCGROWTHCONDITIONS
concentration: 0.2 ppm PGCGROWTHCONDITIONS
concentration: 2 ppm PGCGROWTHCONDITIONS
condition: acetonitrile (control) PGCGROWTHCONDITIONS
condition: myxotoxin PGCGROWTHCONDITIONS
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1 PGCGROWTHCONDITIONS
Mapped reads per annotated gene were counted by Bam2readcount. PGCGROWTHCONDITIONS
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 substr. DH10B PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The reads were processed using BWA software. PGCGROWTHCONDITIONS
toxin: deoxynivalenol PGCGROWTHCONDITIONS
toxin: nivalenol PGCGROWTHCONDITIONS
Culture cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: PNPase mutant PGCGROWTHCONDITIONS
genotype: RNase II mutant PGCGROWTHCONDITIONS
genotype: RNase R mutant PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Exponential Phase PGCGROWTHCONDITIONS
Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin PGCGROWTHCONDITIONS
∆pnp_RNA-Seq PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA. PGCGROWTHCONDITIONS
∆rnb_RNA-Seq PGCGROWTHCONDITIONS
∆rnr_RNA-Seq PGCGROWTHCONDITIONS
strain: K12-MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample … PGCGROWTHCONDITIONS
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database). PGCGROWTHCONDITIONS
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010). PGCGROWTHCONDITIONS
WT_RNA-Seq PGCGROWTHCONDITIONS
common reference (OD600=0.5) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Normalization is performed by TREBAX, using MA-plots. MA-plots can reveal the spot artifacts globally and show the intensity-dependent logarithmic ratio of raw microarray data. In MA-plots, we calculate two parameters, average of logarithmic transferred intensity As=(log(Ts)+log(Rs)) PGCGROWTHCONDITIONS
OD: 0.1 PGCGROWTHCONDITIONS
OD: 0.3 PGCGROWTHCONDITIONS
OD: 0.4 PGCGROWTHCONDITIONS
OD: 0.5 PGCGROWTHCONDITIONS
OD: 0.6 PGCGROWTHCONDITIONS
OD: 1.0 PGCGROWTHCONDITIONS
OD: 1.3 PGCGROWTHCONDITIONS
OD: 1.7 PGCGROWTHCONDITIONS
OD: 2.7 PGCGROWTHCONDITIONS
OD: 4.5 PGCGROWTHCONDITIONS
OD: 4.7 PGCGROWTHCONDITIONS
OD: 4.8 PGCGROWTHCONDITIONS
Qiagen RNeasy mini Kit PGCGROWTHCONDITIONS
Reference Design timecourse c_t10.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t10.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t1.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t11.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t11.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t1.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t2.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t2.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t3.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t3.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t4.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t4.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t5.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t5.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t6.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t6.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t7.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t7.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t8.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t8.2 PGCGROWTHCONDITIONS
Reference Design timecourse c_t9.1 PGCGROWTHCONDITIONS
Reference Design timecourse c_t9.2 PGCGROWTHCONDITIONS
Strain: W3110 PGCGROWTHCONDITIONS
time 10 (OD600=4.7) PGCGROWTHCONDITIONS
time 11 (OD600=4.8) PGCGROWTHCONDITIONS
time 1 (OD600=0.1) PGCGROWTHCONDITIONS
time 2 (OD600=0.3) PGCGROWTHCONDITIONS
time 3 (OD600=0.4) PGCGROWTHCONDITIONS
time 4 (OD600=0.6) PGCGROWTHCONDITIONS
time 5 (OD600=1.0) PGCGROWTHCONDITIONS
time 6 (OD600=1.3) PGCGROWTHCONDITIONS
time 7 (OD600=1.7) PGCGROWTHCONDITIONS
time 8 (OD600=2.7) PGCGROWTHCONDITIONS
time 9 (OD600=4.5) PGCGROWTHCONDITIONS
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99. PGCGROWTHCONDITIONS
All strains used are E. coli K-12 MG1655 and its derivatives. Glycerol stock of the E. coli strain was inoculated into 3 mL Luria broth supplemented with 150 μg kanamycin and cultured overnight at 37°C with constant agitation. PGCGROWTHCONDITIONS
ArgR (-arg) rep1 and rep2 PGCGROWTHCONDITIONS
ArgR (+arg) rep1 and rep2 PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.4 PGCGROWTHCONDITIONS
chip antibody: Anti-myc (9E10) (Santa Cruz, Dallas, TX) PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Cultured cells (50 mL) were cross-linked with 1% formaldehyde at room temperature for 30 min and added 2 mL of 2.5M glycine to quench the unused formaldehyde. After washing  three times with 50 mL of ice-cold Tris-buffered saline (TBS), the washed cells were resuspended in 0.5 mL of lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 μg PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: gff file is generated by in-house script PGCGROWTHCONDITIONS
The cross-linked DNA-ArgR complexes in the supernatant were then immunoprecipitated by adding 10 µL of Anti-myc (9E10) (Santa Cruz, Dallas, TX). For mock-IP control, 2 µg of normal mouse IgG (Santa Cruz) was added into the supernatant in parallel. They were then incubated overnight at 4oC with constant rotation. The cross-linked DNA-protein and antibody complexes were selectively captured by adding 50 µL of Dynabeads Pan Mouse IgG magnetic beads (Invitrogen, Grand Island, NY). Then, DNAs were end-polished using T4 DNA polymerase (NEB, Ipswich, MA), ligated with the annealed adaptor 1 (5’- Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT and 5’- OH-AGATCGGAAGAGC-OH), nick-repaired using phi29 polymerase (NEB), and digested with λ exonuclease (NEB) as reported previously. Then, protein-DNA complexes were reverse-cross-linked by heating at 65°C overnight and proteins were degraded by 8 µg of protease K (Invitrogen). The purified DNAs were denatured at 95°C and extended by P1 primer (5’-OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT), further ligated with the annealed adaptor 2 (5’-OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT and 5’-OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG). The ligated DNA products were purified using Qiagen PCR purification kit and were PCR-amplified by P2 primer (5’-OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and P3 primer (5’-OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT). The degenerative sequence (the underlined 6Ns) in the P3 primer indicates the index sequence for the Illumina next-generation sequencing (Illumina, San Diego, CA). The PCR-amplified DNA products were then loaded onto 2% agarose gel and extracted using QIAquick gel purification columns. PGCGROWTHCONDITIONS
The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g PGCGROWTHCONDITIONS
To capture target protein binding sites corresponding genomic position of mapped reads start position (MRSP) was counted and stored for visual inspection using in-house scripts. PGCGROWTHCONDITIONS
cDNA_A_cy3 PGCGROWTHCONDITIONS
cDNA_B_cy5 PGCGROWTHCONDITIONS
E. coli MG1655 genomic DNA PGCGROWTHCONDITIONS
E. coli MG1655 RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gDNA_A_cy5 PGCGROWTHCONDITIONS
gDNA_B_cy3 PGCGROWTHCONDITIONS
Genomic DNA was purified using a 20 PGCGROWTHCONDITIONS
Linearly scaled so that intensity values in gDNA_A_cy5, cDNA_A_cy3, gDNA_B_cy3, and cDNA_B_cy5 are comparable PGCGROWTHCONDITIONS
Strain MG1655 PGCGROWTHCONDITIONS
Total RNA was purified on a RNeasy columns (Qiagen); ribosomal RNAs were removed with the MicroExpress kit (Ambion). The resulting RNA was reverse transcribed with SuperScript II reverse transcriptase (Invitrogen) + random hexamers + dNTP mix containing aminoallyl-dUTP. PGCGROWTHCONDITIONS
Beta_ChIP_A_cy5 PGCGROWTHCONDITIONS
Beta_ChIP_B_cy5 PGCGROWTHCONDITIONS
Beta_ChIP_control_A_cy3 PGCGROWTHCONDITIONS
Beta_ChIP_control_B_cy3 PGCGROWTHCONDITIONS
Cells were fixed in 1% formaldehyde at room temperature for 20 min, quenched with glycine, and lysed. Chromatin was pelleted and solublized by sonication. PGCGROWTHCONDITIONS
Cells were fixed in 1% formaldehyde at room temperature for 20 min, quenched with glycine, and lysed. Chromatin was pelleted and solublized by sonication. Crosslinked chromatin was then immunoprecipitated. PGCGROWTHCONDITIONS
E. coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Linearly scaled so that intensity values in Sigma70_ChIP_control_A_cy3, Sigma70_ChIP_A_cy5, Sigma70_ChIP_control_B_cy3, Sigma70_ChIP_B_cy5, Beta_ChIP_control_A_cy3, Beta_ChIP_A_cy5, Beta_ChIP_control_B_cy3, Beta_ChIP_B_cy5 are comparable PGCGROWTHCONDITIONS
Sigma70_ChIP_A_cy5 PGCGROWTHCONDITIONS
Sigma70_ChIP_B_cy5 PGCGROWTHCONDITIONS
Sigma70_ChIP_control_A_cy3 PGCGROWTHCONDITIONS
Sigma70_ChIP_control_B_cy3 PGCGROWTHCONDITIONS
Strain MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Normalization is performed by TREBAX, using MA-plots. MA-plots can reveal the spot artifacts globally and show the intensity-dependent logarithmic ratio of raw microarray data. In MA-plots, we calculate two parameters, average of logarithmic transferred intensity As=(log(Ts)+log(Rs)) PGCGROWTHCONDITIONS
OD :0.1 PGCGROWTHCONDITIONS
OD :0.3 PGCGROWTHCONDITIONS
OD :0.4 PGCGROWTHCONDITIONS
OD :0.6 PGCGROWTHCONDITIONS
OD: 0.6 PGCGROWTHCONDITIONS
OD :1.0 PGCGROWTHCONDITIONS
OD :1.3 PGCGROWTHCONDITIONS
OD :1.7 PGCGROWTHCONDITIONS
OD :2.7 PGCGROWTHCONDITIONS
OD :4.5 PGCGROWTHCONDITIONS
OD 4.5 PGCGROWTHCONDITIONS
OD :4.7 PGCGROWTHCONDITIONS
OD :4.8 PGCGROWTHCONDITIONS
OD :OD 0.1 PGCGROWTHCONDITIONS
Qiagen RNeasy mini Kit PGCGROWTHCONDITIONS
Sequential Design timecourse t10_t11.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t10_t11.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t1_t2.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t1_t2.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t2_t3.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t2_t3.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t3_t4.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t3_t4.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t4_t5.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t4_t5.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t5_t6.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t5_t6.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t6_t7.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t6_t7.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t7_t8.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t7_t8.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t8_t9.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t8_t9.2 PGCGROWTHCONDITIONS
Sequential Design timecourse t9_t10.1 PGCGROWTHCONDITIONS
Sequential Design timecourse t9_t10.2 PGCGROWTHCONDITIONS
Strain W3110 PGCGROWTHCONDITIONS
Strain :W3110 PGCGROWTHCONDITIONS
Strain : W3110 PGCGROWTHCONDITIONS
Strain: W3110 PGCGROWTHCONDITIONS
Strian :W3110 PGCGROWTHCONDITIONS
time 10 (OD600=4.7) PGCGROWTHCONDITIONS
time 11 (OD600=4.8) PGCGROWTHCONDITIONS
time 1 (OD600=0.1) PGCGROWTHCONDITIONS
time 2 (OD600=0.3) PGCGROWTHCONDITIONS
time 3 (OD600=0.4) PGCGROWTHCONDITIONS
time 4 (OD600=0.6) PGCGROWTHCONDITIONS
time 5 (OD600=1.0) PGCGROWTHCONDITIONS
time 6 (OD600=1.3) PGCGROWTHCONDITIONS
time 7 (OD=1.7) PGCGROWTHCONDITIONS
time 7 (OD600=1.7) PGCGROWTHCONDITIONS
time 8 (OD=2.7) PGCGROWTHCONDITIONS
time 8 (OD600=2.7) PGCGROWTHCONDITIONS
time 9 (OD600=4.5) PGCGROWTHCONDITIONS
E. coli HB101 grown in Terrific broth media for 12 hours were washed three times in sdH2O and re-suspended in S-Basal complete medium. PGCGROWTHCONDITIONS
E. coli were incubated in S-Basal complete medium alone or in the presence of C. elegans, Giardia conditioned meida, and both C. elegans and Giardia conditioned media. PGCGROWTHCONDITIONS
Escherchia coli HB101 PGCGROWTHCONDITIONS
Escherchia coli HB101 exposed to C. elegans and Giardia for 24 hours PGCGROWTHCONDITIONS
Escherchia coli HB101 exposed to C. elegans for 24 hours PGCGROWTHCONDITIONS
Escherchia coli HB101 exposed to Giardia for 24 hours PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: E. coli [supE44 hsdS20(rB-mB-) recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1] PGCGROWTHCONDITIONS
HB101, biological rep2 PGCGROWTHCONDITIONS
HB101, biological rep3 PGCGROWTHCONDITIONS
HB101, exposed to C. elegans and Giardia, biological rep1 PGCGROWTHCONDITIONS
HB101, exposed to C. elegans and Giardia, biological rep2 PGCGROWTHCONDITIONS
HB101, exposed to C. elegans and Giardia, biological rep3 PGCGROWTHCONDITIONS
HB101, exposed to C. elegans, biological rep1 PGCGROWTHCONDITIONS
HB101, exposed to C. elegans, biological rep2 PGCGROWTHCONDITIONS
HB101, exposed to C. elegans, biological rep3 PGCGROWTHCONDITIONS
HB101, exposed to Giardia, biological rep1 PGCGROWTHCONDITIONS
HB101, exposed to Giardia, biological rep2 PGCGROWTHCONDITIONS
HB101, exposed to Giardia, biological rep3 PGCGROWTHCONDITIONS
strain: HB101 PGCGROWTHCONDITIONS
The microarray data files were processed using statistical software R version 3.0.1 and Bioconductor packages. The Single-Channel Array Normalization (SCAN.UPC) package was used to normalize the microarray data. Batch effects were adjusted by using the Empirical Bayes method implemented in COMBAT software. PGCGROWTHCONDITIONS
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to instructions in the kit. PGCGROWTHCONDITIONS
CEL files were quantified with Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2. PGCGROWTHCONDITIONS
E. coli BW25113 were maintained in Luria-Bertani medium at 37ºC for about 14 h until they reached the stationary phase of cell growth before treatment. PGCGROWTHCONDITIONS
E. coli incubated with GST-fused Drosophila immune proteins for 10 min PGCGROWTHCONDITIONS
E. coli incubated with GST-fused Drosophila immune proteins for 10 min, biological rep1 PGCGROWTHCONDITIONS
E. coli incubated with GST-fused Drosophila immune proteins for 10 min, biological rep2 PGCGROWTHCONDITIONS
E. coli incubated with GST-fused Drosophila immune proteins for 10 min, biological rep3 PGCGROWTHCONDITIONS
E. coli incubated with GST protein alone for 10 min PGCGROWTHCONDITIONS
E. coli incubated with GST protein for 10 min, biological rep1 PGCGROWTHCONDITIONS
E. coli incubated with GST protein for 10 min, biological rep2 PGCGROWTHCONDITIONS
E. coli incubated with GST protein for 10 min, biological rep3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
incubated with: Drosophila immune proteins PGCGROWTHCONDITIONS
incubated with: GST alone (3 μM; control) PGCGROWTHCONDITIONS
incubation duration: 10 min PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
The E. coli strain BW25113 (2 x 10^9) suspended with insect saline (0.13 M NaCl, 4.7 mM KCl, 1.9 mM CaCl2), was incubated with GST or GST-fused Drosophila immune proteins for 10 min at room temperature. PGCGROWTHCONDITIONS
Total RNA was purified with an RNeasy micro kit (Qiagen K.K., Tokyo, Japan). PGCGROWTHCONDITIONS
cDNA were synthesized from the reverse transcription of Total RNA using the Life Technologies SuperScript II Double-Strand Synthesis Kit PGCGROWTHCONDITIONS
E. coli MG1655 Cold Shock PGCGROWTHCONDITIONS
E. coli MG1655 Cold Shock was grown at 15°C for 4 hour then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media. PGCGROWTHCONDITIONS
E. coli MG1655 Heat Shock PGCGROWTHCONDITIONS
E. coli MG1655 Heat Shock was grown at 50°C for 4 hour then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media. PGCGROWTHCONDITIONS
E. coli MG1655 Low pH PGCGROWTHCONDITIONS
E. coli MG1655 Low pH was grown at 37°C for 1 hour in LB media with pH4.5 then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media. PGCGROWTHCONDITIONS
E. coli MG1655 minimal C PGCGROWTHCONDITIONS
E. coli MG1655 minimal C&N PGCGROWTHCONDITIONS
E. coli MG1655 minimal C&N Source was grown untill reach to quater of O.D.600nm of Standard sample at 37°C in minimal C and N source MOPS media(C-N- MOPS). PGCGROWTHCONDITIONS
E. coli MG1655 minimal C Source was grown untill reach to half of O.D.600nm of Standard sample at 37°C in minimal C source MOPS media(C- MOPS). PGCGROWTHCONDITIONS
E. coli MG1655 minimal N PGCGROWTHCONDITIONS
E. coli MG1655 minimal N Source was grown untill reach to half of O.D.600nm of Standard sample at 37°C in minimal N source MOPS media(N- MOPS). PGCGROWTHCONDITIONS
E. coli MG1655 Osmotic stress PGCGROWTHCONDITIONS
E. coli MG1655 Osmotic Stress was grown untill reach to half of O.D.600nm of Standard sample at 37°C in 45ml MOPS media with 6ml 4M Sodium Chloride. PGCGROWTHCONDITIONS
E. coli MG1655 Oxidative stress PGCGROWTHCONDITIONS
E. coli MG1655 Oxidative Stress was grown untill reach to half of O.D.600nm of Standard sample at 37°C in 49ml MOPS media with 400μl 7% Hydrogen peroxide. PGCGROWTHCONDITIONS
E. coli MG1655 Standard PGCGROWTHCONDITIONS
E. coli MG1655 Standard was grown to mid-log phase (O.D.600nm 0.6~0.8) at 37°C in LB media. PGCGROWTHCONDITIONS
E. coli MG1655 UV PGCGROWTHCONDITIONS
E. coli MG1655 UV was exposed to UV light for 15 minutes then grown untill reach to half of O.D.600nm of Standard sample at 37°C in LB media. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
MG1655_standard_condition_rep1 PGCGROWTHCONDITIONS
MG1655_standard_condition_rep2 PGCGROWTHCONDITIONS
MG1655_under_ColdShock_rep1 PGCGROWTHCONDITIONS
MG1655_under_ColdShock_rep2 PGCGROWTHCONDITIONS
MG1655_under_HeatShock_rep2 PGCGROWTHCONDITIONS
MG1655_under_Low_pH_rep1 PGCGROWTHCONDITIONS
MG1655_under_minimal_C&N_source_rep1 PGCGROWTHCONDITIONS
MG1655_under_minimal_C&N_source_rep2 PGCGROWTHCONDITIONS
MG1655_under_minimal_C_source_rep1 PGCGROWTHCONDITIONS
MG1655_under_minimal_C_source_rep2 PGCGROWTHCONDITIONS
MG1655_under_minimal_N_source_rep1 PGCGROWTHCONDITIONS
MG1655_under_minimal_N_source_rep2 PGCGROWTHCONDITIONS
MG1655_under_Osmotic_Stress_rep1 PGCGROWTHCONDITIONS
MG1655_under_Osmotic_Stress_rep2 PGCGROWTHCONDITIONS
MG1655_under_Oxidative_Stress_rep1 PGCGROWTHCONDITIONS
MG1655_under_Oxidative_Stress_rep2 PGCGROWTHCONDITIONS
MG1655_UV_Treatment_rep1 PGCGROWTHCONDITIONS
MG1655_UV_Treatment_rep2 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleGen Deva software, version 1.2 (Roche NimbleGen, Inc.). PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA  concentration was measured by SpectorPhotometer(NonoDrop). PGCGROWTHCONDITIONS
treatment: Cold Shock PGCGROWTHCONDITIONS
treatment: Heat Shock PGCGROWTHCONDITIONS
treatment: Low pH PGCGROWTHCONDITIONS
treatment: minimal C&N source PGCGROWTHCONDITIONS
treatment: minimal C source PGCGROWTHCONDITIONS
treatment: minimal N source PGCGROWTHCONDITIONS
treatment: Osmotic stress PGCGROWTHCONDITIONS
treatment: Oxidative stress PGCGROWTHCONDITIONS
treatment: Standard PGCGROWTHCONDITIONS
treatment: UV PGCGROWTHCONDITIONS
Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 10^8 cells PGCGROWTHCONDITIONS
condition: exponential growth, 36.9ºC PGCGROWTHCONDITIONS
condition: exponential growth, 41.2ºC PGCGROWTHCONDITIONS
condition: exponential growth, 43.2ºC PGCGROWTHCONDITIONS
condition: exponential growth, 44.8ºC PGCGROWTHCONDITIONS
condition: heat shock response, 44.8ºC PGCGROWTHCONDITIONS
E. coli 37L evolved strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 37L evolved strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 37L evolved strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, evolutionary temperature, rep 1 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, evolutionary temperature, rep 2 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, evolutionary temperature, rep 3 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, regular temperature, rep 1 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, regular temperature, rep 2 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, regular temperature, rep 3 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, under 41ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, under 41ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 41B evolved strain, under 41ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 41B strain, 30 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 41B strain, 30 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 41B strain, 5 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 41B strain, 5 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 41B strain, heat shock, long, rep 1 PGCGROWTHCONDITIONS
E. coli 41B strain, heat shock, long, rep 2 PGCGROWTHCONDITIONS
E. coli 41B strain, heat shock, rep 1 PGCGROWTHCONDITIONS
E. coli 41B strain, heat shock, rep 2 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, evolutionary temperature, rep 1 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, evolutionary temperature, rep 2 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, evolutionary temperature, rep 3 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, regular temperature, rep 1 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, regular temperature, rep 2 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, regular temperature, rep 3 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, under 43ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, under 43ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 43B evolved strain, under 43ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 43B strain, 30 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 43B strain, 30 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 43B strain, 5 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 43B strain, 5 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 43B strain, heat shock, long, rep 1 PGCGROWTHCONDITIONS
E. coli 43B strain, heat shock, long, rep 2 PGCGROWTHCONDITIONS
E. coli 43B strain, heat shock, rep 1 PGCGROWTHCONDITIONS
E. coli 43B strain, heat shock, rep 2 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, evolutionary temperature, rep 1 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, evolutionary temperature, rep 2 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, evolutionary temperature, rep 3 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, regular temperature, rep 1 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, regular temperature, rep 2 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, regular temperature, rep 3 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, under 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, under 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 45L evolved strain, under 45ºC, rep 3 PGCGROWTHCONDITIONS
E. coli 45L strain, 30 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 45L strain, 30 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 45L strain, 5 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli 45L strain, 5 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli 45L strain, heat shock, long, rep 1 PGCGROWTHCONDITIONS
E. coli 45L strain, heat shock, long, rep 2 PGCGROWTHCONDITIONS
E. coli 45L strain, heat shock, rep 1 PGCGROWTHCONDITIONS
E. coli 45L strain, heat shock, rep 2 PGCGROWTHCONDITIONS
E. coli ancestor strain, 30 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli ancestor strain, 30 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli ancestor strain, 5 min heat shock at 45ºC, rep 1 PGCGROWTHCONDITIONS
E. coli ancestor strain, 5 min heat shock at 45ºC, rep 2 PGCGROWTHCONDITIONS
E. coli ancestor strain, under 37ºC, rep 1 PGCGROWTHCONDITIONS
E. coli ancestor strain, under 37ºC, rep 2 PGCGROWTHCONDITIONS
E. coli ancestor strain, under 37ºC, rep 3 PGCGROWTHCONDITIONS
E. coli Anc strain, heat shock, long, rep 1 PGCGROWTHCONDITIONS
E. coli Anc strain, heat shock, long, rep 2 PGCGROWTHCONDITIONS
E. coli Anc strain, heat shock, rep 1 PGCGROWTHCONDITIONS
E. coli Anc strain, heat shock, rep 2 PGCGROWTHCONDITIONS
E. coli Anc strain, regular temperature, rep 1 PGCGROWTHCONDITIONS
E. coli Anc strain, regular temperature, rep 2 PGCGROWTHCONDITIONS
E. coli Anc strain, regular temperature, rep 3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). PGCGROWTHCONDITIONS
strain: DH1ΔleuB::gfpuv5-kmr PGCGROWTHCONDITIONS
The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 7,000 × g for 3 min at 4°C, and the pelleted cells were stored at –80°C prior to use. PGCGROWTHCONDITIONS
The normalized data can be found on the series record in the file \GSE61749_Normalized_data.txt\. The data values presented in this file are log10 mRNA concentration (pM). PGCGROWTHCONDITIONS
Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions. PGCGROWTHCONDITIONS
7 h 7HI biofilm cells PGCGROWTHCONDITIONS
7 h biofilm cells PGCGROWTHCONDITIONS
7 h isatin biofilm cells PGCGROWTHCONDITIONS
7 h suspension cells PGCGROWTHCONDITIONS
EHEC LB 7 h 7HI biofilm cells PGCGROWTHCONDITIONS
EHEC LB 7 h biofilm cells PGCGROWTHCONDITIONS
EHEC LB 7 h isatin biofilm cells PGCGROWTHCONDITIONS
EHEC LB 7 h suspension cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of EHEC wild type after 7h of growth in LB and 0.1 % DMF with glass wool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of EHEC wild type after 7h of growth in LB and 1000 micro M 7-hydroxyindole with glass wool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of EHEC wild type after 7h of growth in LB and 250 micro M isatin with glass wool PGCGROWTHCONDITIONS
RNA extracted from suspension cells of EHEC wild type after 7 h of growth in LB and 0.1 % DMF with glass wool PGCGROWTHCONDITIONS
To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia PGCGROWTHCONDITIONS
cDNA library of the nascent RNA was constructed according to Churchman and Weissman, Nature 2011 (PMID: 21248844). PGCGROWTHCONDITIONS
Each tube of the cell pellet stored at -80˚C was resuspended in 650 ml TES buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.1% TritonX 100, 0.3 mM PMSF) at room temperature (RT). The cell suspension was mixed with 100 kU Ready-Lyse Lysozyme (Epicentre) and 50 µg RNaseA (Sigma) and incubated for 5 min, allowing rapid cell lysis. To digest the nucleoide, 62.5 U DNaseI (Roche) and 250 µg PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
molecule subtype: nascent 3' RNA PGCGROWTHCONDITIONS
Pause sites in E. coli wild-type strain identified by RNET-seq PGCGROWTHCONDITIONS
Pause sites in E. coli ΔgreAB strain identified by RNET-seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
The 200 ml eluate from the Ni-NTA agarose was mixed with equal volume of pre-warmed PCI and incubated for 2 min at 70˚C. The mixture was centrifuged, and RNA and DNA were precipitated with isopropanol from the supernatant. The pellet was dissolved in 30 ml DNase I buffer with 5 U DNaseI (Takara Bio) and 20 U SUPERase, incubated for 10 min at RT. RNA was separated from the digested DNA by the PCI extraction and RNA was precipitated with isopropanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis. PGCGROWTHCONDITIONS
The cells were grown in ~300 ml LB broth +25 mg PGCGROWTHCONDITIONS
The fastq files of 36-bp sequenced reads were generated with the CASAVA v1.8 (Illumina). For the bulk RNET-seq analysis, the specific adapter sequences were trimmed with the Trimmomatic v0.25 to obtain reads ≥ 21-nt from the 5’ end. The reads ≥ 21-nt were mapped to the reference genome of E. coli K-12 strain W3110 (NC_007779.1) using the Bowtie2 v2.1.0 with the default parameter. A gene annotation file of E. coli W3110 was downloaded from the ftp server of Ensembl. PGCGROWTHCONDITIONS
The processed data file (csv) includes information about genomic position, reference PGCGROWTHCONDITIONS
To analyze RNAP pausing on the E. coli chromosome, we counted the number of reads at every genomic nucleotide position using the mpileup command of SAM tools v0.1.18 with –A –B parameters. Pausing sites were defined P(φ, δ), where φ is the minimal fraction of having 3’ RNA ends in the mapped reads and δ is the minimal read depth for any genomic position. We chose δ to be 100 for WT and 160 for ΔgreAB, which normalized these respective numbers for each strain since there were 1.6-fold more total reads in the ΔgreAB strain. The high φ parameter allowed us to define a reliable pause-inducing element for WT or ΔgreAB cells. PGCGROWTHCONDITIONS
W3110 rpoC-6xHis::kan gal490 PGCGROWTHCONDITIONS
W3110 rpoC-6xHis::kan greA::tet, greB::amp PGCGROWTHCONDITIONS
10 μg of total RNA sample was subjected to purification for discarding rRNA via the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. Following purification, the RNA was interrupted into short fragments using divalent cations under elevated temperature and the short fragments were used for the cDNA synthesis using a SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s instructions. These cDNA fragments were purified with a QIAquick PCR purification kit (Qiagen), and then went through end reparation, adding poly(A) and ligation of sequencing adaptors. These products were purified with agarose gel electrophoresis and fragments in the size of 200-250 bp were selected for PCR amplification to construct the cDNA library. PGCGROWTHCONDITIONS
All those uniquely mapped reads were used to calculate the gene expression level by the RPKM method, which is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression and thus the calculated gene expression level can be directly used for comparing the difference of gene expression among samples. PGCGROWTHCONDITIONS
Bacterium PGCGROWTHCONDITIONS
Base calling performed using  Illumina GA pipeline 1.6. PGCGROWTHCONDITIONS
cas_RNAA PGCGROWTHCONDITIONS
con_RNAA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM666v1; NC_002655.2 PGCGROWTHCONDITIONS
In order to generate the VBNC state in E. coli O157:H7, 20 mL of the exponential-phase cell suspensions in a 50 mL sterile glass tube was treated by HPCD at 5 MPa and 25℃ for 40 min. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: O157:H7 NCTC 12900 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft excel spreadsheet files include RPKM values for each gene of sample PGCGROWTHCONDITIONS
The clean reads obtained were aligned to the genome sequence of E. coli O157:H7 EDL933 using SOAP2 PGCGROWTHCONDITIONS
The raw reads were filtered for removing dirty raw reads which contain adapters, unknown or low quality bases. PGCGROWTHCONDITIONS
The strain was stocked in tryptic soy broth (TSB) with 25% glycerol at -80℃, and was activated by streaking onto TSA plate and incubating at 37℃ for 24 h. And then, a single colony was picked and used to inoculate TSB and incubated at 37℃ for 12 h with shaking at 200 rpm. This overnight culture was transferred to TSB at a dilution of 1:100 and grew to the exponential phase (OD550=0.93). PGCGROWTHCONDITIONS
Total RNA was isolated from the VBNC cells and the exponential-phase cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA samples were treated with DNase Ⅰ (Invitrogen) to remove residual genomic DNA. PGCGROWTHCONDITIONS
treatment: None PGCGROWTHCONDITIONS
treatment: Treated by HPCD at 5 MPa and 25℃ for 40 min PGCGROWTHCONDITIONS
bacterial cells grown to OD600=0.5 PGCGROWTHCONDITIONS
Bacterial strains were grown in LB. Overnight cultures were diluted 1:100 in fresh LB and grown at 37°C with shaking to an OD600 = 0.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GPR files were analyzed further with Acuity 4.0 software (Molecular Devices, USA) starting with lowess normalization. Normalized log2 ratio data from biological replicates and technical replicates (dye swap) were averaged and the statistical significance (p-value) was calculated. PGCGROWTHCONDITIONS
recA730_vs_recA730,dcd PGCGROWTHCONDITIONS
recA730_vs_recA730,ndk PGCGROWTHCONDITIONS
RNA was isolated using the RNeasy Protect Bacteria Mini Kit (Qiagen), following manufacturer's instructions. PGCGROWTHCONDITIONS
strain: MC4100 derivative PGCGROWTHCONDITIONS
strain: MC4100 derivative, dcd::kan PGCGROWTHCONDITIONS
strain: MC4100 derivative, ndk::cam PGCGROWTHCONDITIONS
strain: MC4100 derivative, recA730 PGCGROWTHCONDITIONS
strain: MC4100 derivative, recA730, dcd::kan PGCGROWTHCONDITIONS
strain: MC4100 derivative, recA730, ndk::cam PGCGROWTHCONDITIONS
WT_vs_dcd PGCGROWTHCONDITIONS
WT_vs_ndk PGCGROWTHCONDITIONS
WT_vs_recA730 PGCGROWTHCONDITIONS
50 OD600 of bacteria have been grown to the desired growth stage and harvested by centrifugation. They were lysed in 500 µl of the lysis buffer (20 mM Tris-HCl, pH7.5, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1 mM PMSF, 0.2% Triton X100, 20 U PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Coverage calculation and normalisation (via READemption) PGCGROWTHCONDITIONS
Demultiplexing PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia ProQ coIP PGCGROWTHCONDITIONS
Escherichia ProQ Lysate PGCGROWTHCONDITIONS
Escherichia WT coIP PGCGROWTHCONDITIONS
Escherichia WT Lysate PGCGROWTHCONDITIONS
Fastq quality trimming using FastX and a cut-off value of 20 PGCGROWTHCONDITIONS
Fastq to fasta conversion using FastX PGCGROWTHCONDITIONS
Genome_build: NC_007779.1 PGCGROWTHCONDITIONS
LB, 37°C, 220 rpm, OD600=0.5, 2.0, 2.0+6 h PGCGROWTHCONDITIONS
Read mapping using segemehl (via READemption) PGCGROWTHCONDITIONS
rip antibody: Monoclonal ANTI-FLAG^=AE M2 antibody produced in mouse, Sigma, F1804-200UG,SLBG5673V PGCGROWTHCONDITIONS
RIP-Seq PGCGROWTHCONDITIONS
RNA-seq libraries were prepared by Vertis AG (Freising-Weihenstephan, Germany). Briefly, RNA was polyadenylated with poly(A) polymerase, 5’-triphosphates were removed with tobacco acid pyrophosphatase followed by ligation of a 5’-adapter. First-strand cDNA synthesis was performed with the use of an oligo(dT) barcoded adapter primer and the M-MVL reverse transcriptase. The resulting cDNA was PCR-amplified with a high fidelity DNA polymerase. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics). PGCGROWTHCONDITIONS
Size filtering: discarding reads shorter than 12 nt (via READemption) PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle PGCGROWTHCONDITIONS
The equivalent of 5 OD600 was saved for RNA extraction with TriZOL before adding antibodies (lysate RNA sample). For coIP samples, beads were resuspended in the lysis buffer, mixed with an equal volume of phenol:chloroform:isopropanol (25:24:1, pH4.5, Roth) for 20 s and incubated at room temperature for 3 min. After centrifugation, the aqueous phase was precipitated with isopropanol (coIP RNA sample). The purified RNA coIP sample was treated with DNase I (Thermo Scientific) to remove the residual DNA and reisolated with phenol:chloroform:isopropanol. The spike-in RNA (5’P-CUCGUCCGACGUCACCUAGA, IBA) had been added to 40 pg PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
AT1 biological replicate PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
LB mRNA PGCGROWTHCONDITIONS
LB mRNA biological replicate PGCGROWTHCONDITIONS
LB mRNA technical replicate PGCGROWTHCONDITIONS
LB RPF PGCGROWTHCONDITIONS
LB RPF biological replicate PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: AT1 digested total RNA PGCGROWTHCONDITIONS
sample type: ribosome protected PGCGROWTHCONDITIONS
sample type: V1 digested total RNA PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
strain: MC4101 PGCGROWTHCONDITIONS
strain: MC4102 PGCGROWTHCONDITIONS
strain: MC4103 PGCGROWTHCONDITIONS
strain: MC4104 PGCGROWTHCONDITIONS
strain: MC4105 PGCGROWTHCONDITIONS
strain: MC4106 PGCGROWTHCONDITIONS
strain: MC4107 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A PGCGROWTHCONDITIONS
V1 biological replicate PGCGROWTHCONDITIONS
At OD450 = 0.3, cultures induced with 1 mM IPTG. Cells harvested 20 min after induction PGCGROWTHCONDITIONS
Cells harvested at OD450 = 0.3 PGCGROWTHCONDITIONS
Culture samples for microarray analysis were added to ice-cold 5% water-saturated phenol in ethanol solution, centrifuged at 6,600 g and the cell pellets flash frozen in liquid N2 before storing at -80 degrees C until required. Total RNA was isolated from the stored cell pellets using the hot phenol method, and labeled Cy3 and Cy5 cDNA was prepared from 16 ug total RNA with 10 ug random hexamer (Integrated DNA Technologies, Inc., Coralville, IA, USA). PGCGROWTHCONDITIONS
Data filtered for PCR success, >3x local background and spot quality (GenePix Flag). Normalized using Lowess smoothing from MA plot PGCGROWTHCONDITIONS
delta hfq PGCGROWTHCONDITIONS
Delta hfq PGCGROWTHCONDITIONS
Delta rseA PGCGROWTHCONDITIONS
EC12n097 delta rseA PGCGROWTHCONDITIONS
EC12n098 delta rseA PGCGROWTHCONDITIONS
EC12n099 delta rseA PGCGROWTHCONDITIONS
EC18n018 hfq+ rpoE overexpression 20 min PGCGROWTHCONDITIONS
EC18n019 hfq- rpoE overexpression 20 min PGCGROWTHCONDITIONS
EC18n035 delta rseA PGCGROWTHCONDITIONS
EC18n036 delta rseA PGCGROWTHCONDITIONS
EC18n037 delta hfq PGCGROWTHCONDITIONS
EC18n038 delta hfq PGCGROWTHCONDITIONS
EC18n039 delta hfq PGCGROWTHCONDITIONS
EC18n040 delta hfq PGCGROWTHCONDITIONS
EC18n136 hfq+ rpoE overexpression 20 min PGCGROWTHCONDITIONS
Ec18n137 hfq- rpoE overexpression 20 min PGCGROWTHCONDITIONS
EC18n139 hfq+ rpoE overexpression 20 min PGCGROWTHCONDITIONS
EC18n140 hfq- rpoE overexpression 20 min PGCGROWTHCONDITIONS
EC19n075 delta hfq PGCGROWTHCONDITIONS
EC19n076 delta hfq PGCGROWTHCONDITIONS
EC19n098 delta hfq PGCGROWTHCONDITIONS
EC19n099 delta hfq PGCGROWTHCONDITIONS
EC19n100 delta rseA PGCGROWTHCONDITIONS
EC19n101 delta rseA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Hfq- RpoE overexpression (20 min) PGCGROWTHCONDITIONS
hfq+ Wild type control (20 min) PGCGROWTHCONDITIONS
M9 minimal complete media, cultures grown aerobically at 30 degrees C in a gyratory water bath shaking at 240 rpm PGCGROWTHCONDITIONS
MG1655 rpoHp3::lacZ delta lacX74 PGCGROWTHCONDITIONS
MG1655 rpoHp3::lacZ delta lacX74 hfq1::omega(Km;BclI) (hfq-) PGCGROWTHCONDITIONS
MG1655 rpoHp3::lacZ delta lacX74 hfq2::omega(Km;KpnI) (hfq+) PGCGROWTHCONDITIONS
MG1655 rpoHp3::lacZ delta lacX74 nadB::Tn10 drseA PGCGROWTHCONDITIONS
RpoE induced (20 min) PGCGROWTHCONDITIONS
Wild type control PGCGROWTHCONDITIONS
Wild type control (20 min) PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were crosslinked in 1% formadehyde for 25 min at room temperature followed by 5 minutes of quenching with glycine. Cells were washed 3X with ice cold TBS. Cell pellets were stored at -80 C. PGCGROWTHCONDITIONS
Cells were enyzmatically lysed in the presence of protease inhibitors prior to fragmentation using sonication. Protein PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
chip antibody: c-Myc Antibody (9E10), Santa Cruz Biotech, sc-40 PGCGROWTHCONDITIONS
chip antibody: E. coli CRP Monoclonal Antibody, Neoclone, #N0004 PGCGROWTHCONDITIONS
chip antibody: E. coli RNA Sigma 70 Monoclonal Antibody, Neoclone, #WP004 PGCGROWTHCONDITIONS
ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc PGCGROWTHCONDITIONS
ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc PGCGROWTHCONDITIONS
ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp PGCGROWTHCONDITIONS
ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc PGCGROWTHCONDITIONS
ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc PGCGROWTHCONDITIONS
ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod PGCGROWTHCONDITIONS
ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Chromosomal DNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was based on the method described by Rhee et al. (doi:10.1016 PGCGROWTHCONDITIONS
Peak-calls were done using GPS within the GEMS software package (v2.3) adapted for ChIP-exo data PGCGROWTHCONDITIONS
strain: ArcA8myc PGCGROWTHCONDITIONS
strain: Crp_delAr1 PGCGROWTHCONDITIONS
strain: Crp_delAr1delAr2 PGCGROWTHCONDITIONS
strain: Crp_delAr2 PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
strain: Fnr8myc PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in gff files containing a pileup of 5' tags. GFF column headers \Genbank fna ID, file name, left genomic position, right genomic position, value, strand, extra value, information\ PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_delAr1_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_delAr1_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_delAr1_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_delAr2_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_delAr2_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_delAr2_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_delta-crp_fructose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_delta-crp_fructose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_delta-crp_fructose_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_delta-crp_glucose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_delta-crp_glucose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_delta-crp_glucose_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_delta-crp_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_delta-crp_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_delta-crp_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_wt_fructose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_wt_fructose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_wt_glucose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_wt_glucose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNAseq_wt_glucose_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNAseq_wt_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNAseq_wt_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1 PGCGROWTHCONDITIONS
strain: Crp_delAr1delAr2 PGCGROWTHCONDITIONS
strain: Crp_delAr2 PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
DNeasy (Qiagen) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
gDNA 520 PGCGROWTHCONDITIONS
gDNA 521 PGCGROWTHCONDITIONS
gDNA B02 PGCGROWTHCONDITIONS
gDNA B05 PGCGROWTHCONDITIONS
gDNA C01 PGCGROWTHCONDITIONS
gDNA C02 PGCGROWTHCONDITIONS
gDNA_EColi_520 PGCGROWTHCONDITIONS
gDNA_EColi_521 PGCGROWTHCONDITIONS
gDNA_EColi_B02 PGCGROWTHCONDITIONS
gDNA_EColi_B05 PGCGROWTHCONDITIONS
gDNA_EColi_C01 PGCGROWTHCONDITIONS
gDNA_EColi_C02 PGCGROWTHCONDITIONS
gDNA_EColi_F01 PGCGROWTHCONDITIONS
gDNA_EColi_F02 PGCGROWTHCONDITIONS
gDNA_EColi_H01 PGCGROWTHCONDITIONS
gDNA_EColi_H02 PGCGROWTHCONDITIONS
gDNA_EColi_H03 PGCGROWTHCONDITIONS
gDNA_EColi_H04 PGCGROWTHCONDITIONS
gDNA_EColi_H05 PGCGROWTHCONDITIONS
gDNA_EColi_H12 PGCGROWTHCONDITIONS
gDNA_EColi_H23 PGCGROWTHCONDITIONS
gDNA_EColi_H27 PGCGROWTHCONDITIONS
gDNA_EColi_S04 PGCGROWTHCONDITIONS
gDNA_EColi_S05 PGCGROWTHCONDITIONS
gDNA_EColi_S13 PGCGROWTHCONDITIONS
gDNA F01 PGCGROWTHCONDITIONS
gDNA F02 PGCGROWTHCONDITIONS
gDNA from E.coli K12 cyanine 3 PGCGROWTHCONDITIONS
gDNA H01 PGCGROWTHCONDITIONS
gDNA H02 PGCGROWTHCONDITIONS
gDNA H03 PGCGROWTHCONDITIONS
gDNA H04 PGCGROWTHCONDITIONS
gDNA H05 PGCGROWTHCONDITIONS
gDNA H12 PGCGROWTHCONDITIONS
gDNA H23 PGCGROWTHCONDITIONS
gDNA H27 PGCGROWTHCONDITIONS
gDNA K12 PGCGROWTHCONDITIONS
gDNA S04 PGCGROWTHCONDITIONS
gDNA S05 PGCGROWTHCONDITIONS
gDNA S13 PGCGROWTHCONDITIONS
Local Background Substracted Signal Corrected for unequal Dye incorporation or unequal load of labelled product PGCGROWTHCONDITIONS
strain 520 PGCGROWTHCONDITIONS
strain 521 PGCGROWTHCONDITIONS
strain B02 PGCGROWTHCONDITIONS
strain B05 PGCGROWTHCONDITIONS
strain C01 PGCGROWTHCONDITIONS
strain C02 PGCGROWTHCONDITIONS
strain F01 PGCGROWTHCONDITIONS
strain F02 PGCGROWTHCONDITIONS
strain H01 PGCGROWTHCONDITIONS
strain H02 PGCGROWTHCONDITIONS
strain H03 PGCGROWTHCONDITIONS
strain H04 PGCGROWTHCONDITIONS
strain H05 PGCGROWTHCONDITIONS
strain H12 PGCGROWTHCONDITIONS
strain H23 PGCGROWTHCONDITIONS
strain H27 PGCGROWTHCONDITIONS
strain S04 PGCGROWTHCONDITIONS
strain S05 PGCGROWTHCONDITIONS
strain S13 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli CSH50 PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δfis PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δhns PGCGROWTHCONDITIONS
Fis – 120 min PGCGROWTHCONDITIONS
Fis – 180 min PGCGROWTHCONDITIONS
Fis – 420 min PGCGROWTHCONDITIONS
Fis – 60 min PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-fis PGCGROWTHCONDITIONS
genotype: delta-hns PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
Hns – 120 min PGCGROWTHCONDITIONS
Hns -180 min PGCGROWTHCONDITIONS
Hns – 420 min PGCGROWTHCONDITIONS
Hns – 60 min PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 120 minutes PGCGROWTHCONDITIONS
time: 180 minutes PGCGROWTHCONDITIONS
time: 300 minutes PGCGROWTHCONDITIONS
time: 420 minutes PGCGROWTHCONDITIONS
time: 60 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Wt – 120 min PGCGROWTHCONDITIONS
Wt – 180 min PGCGROWTHCONDITIONS
Wt – 300 min PGCGROWTHCONDITIONS
Wt – 420 min PGCGROWTHCONDITIONS
Wt – 60 min PGCGROWTHCONDITIONS
Bacteria were cultured in an M9 minimal medium supplemented with 2 g PGCGROWTHCONDITIONS
Data analysis was done using R language and environment for a statistical computing and Bioconductor.  Array data were normalized with gcRMA method. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli K-12 tynA- 1h after induction of tynA expression PGCGROWTHCONDITIONS
Escherichia coli K-12 tynA- 4h after the induction of tynA expression PGCGROWTHCONDITIONS
Escherichia coli K-12 tynA- at time of induction of tynA expression PGCGROWTHCONDITIONS
Escherichia coli K-12 wt 1h after the induction of tynA expression PGCGROWTHCONDITIONS
Escherichia coli K-12 wt 4h after the induction of tynA expression PGCGROWTHCONDITIONS
Escherichia coli K-12 wt at time of induction of tynA expression PGCGROWTHCONDITIONS
genotype: tynA- PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Samples were treated with Prokaryotic Target Preparation protocol (GeneChip Expression Analysis Technical Manual). PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
Total RNA was isolated using the RNeasy Mini-Kit (Qiagen) according to the manufacturer`s instruction and DNA was removed by using RNAse-Free DNAse Set (Qiagen). PGCGROWTHCONDITIONS
tynA- at T0 PGCGROWTHCONDITIONS
tynA- at T1h PGCGROWTHCONDITIONS
tynA- at T4h PGCGROWTHCONDITIONS
wt at T0 PGCGROWTHCONDITIONS
wt at T1h PGCGROWTHCONDITIONS
wt at T4h PGCGROWTHCONDITIONS
acetate PGCGROWTHCONDITIONS
chip antibody: anti-myc PGCGROWTHCONDITIONS
chip antibody: anti-rpoB (Santa Cruz Biotech, sc-56766) PGCGROWTHCONDITIONS
chip antibody cat. #: sc-28207 PGCGROWTHCONDITIONS
chip antibody vendor: Santa Cruz Biotech PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
cra-8myc tagged strain_acetate PGCGROWTHCONDITIONS
cra-8myc tagged strain_fructose PGCGROWTHCONDITIONS
cra-8myc tagged strain_glucose PGCGROWTHCONDITIONS
Cra acetate 1 PGCGROWTHCONDITIONS
Cra acetate 2 PGCGROWTHCONDITIONS
Cra fructose 1 PGCGROWTHCONDITIONS
Cra fructose 2 PGCGROWTHCONDITIONS
Cra glucose 1 PGCGROWTHCONDITIONS
Cra glucose 2 PGCGROWTHCONDITIONS
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37C on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4C to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4C to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65C overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55C for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment. PGCGROWTHCONDITIONS
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37oC on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 10 ul of Anti-rpoB mouse antibody was added, and the sample was incubated overnight at 4 oC to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4oC to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65oC overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55 oC for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment. PGCGROWTHCONDITIONS
cultured in: M9 minimal media with 0.2% acetate PGCGROWTHCONDITIONS
cultured in: M9 minimal media with 0.2% fructose PGCGROWTHCONDITIONS
cultured in: M9 minimal media with 0.2% glucose PGCGROWTHCONDITIONS
E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time. PGCGROWTHCONDITIONS
E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
genotype: delta-cra Knock-out strain PGCGROWTHCONDITIONS
genotype: delta-crp Knock-out strain PGCGROWTHCONDITIONS
genotype: Wildtype PGCGROWTHCONDITIONS
growth phase: mid-log PGCGROWTHCONDITIONS
MACE software (https: PGCGROWTHCONDITIONS
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity. PGCGROWTHCONDITIONS
RpoB ∆cra 1 PGCGROWTHCONDITIONS
RpoB ∆cra 2 PGCGROWTHCONDITIONS
RpoB ∆crp 1 PGCGROWTHCONDITIONS
RpoB ∆crp 2 PGCGROWTHCONDITIONS
RpoB WT 1 PGCGROWTHCONDITIONS
RpoB WT 2 PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+ PGCGROWTHCONDITIONS
carbon source: acetate PGCGROWTHCONDITIONS
carbon source: fructose PGCGROWTHCONDITIONS
carbon source: glucose PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0 PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA). PGCGROWTHCONDITIONS
WT_acetate PGCGROWTHCONDITIONS
WT acetate 1 PGCGROWTHCONDITIONS
WT acetate 2 PGCGROWTHCONDITIONS
WT_fructose PGCGROWTHCONDITIONS
WT fructose 1 PGCGROWTHCONDITIONS
WT fructose 2 PGCGROWTHCONDITIONS
WT_glucose PGCGROWTHCONDITIONS
WT glucose 1 PGCGROWTHCONDITIONS
WT glucose 2 PGCGROWTHCONDITIONS
Δcra_acetate PGCGROWTHCONDITIONS
Δcra acetate 1 PGCGROWTHCONDITIONS
Δcra acetate 2 PGCGROWTHCONDITIONS
Δcra_fructose PGCGROWTHCONDITIONS
Δcra fructose 1 PGCGROWTHCONDITIONS
Δcra fructose 2 PGCGROWTHCONDITIONS
Δcra_glucose PGCGROWTHCONDITIONS
Δcra glucose 1 PGCGROWTHCONDITIONS
Δcra glucose 2 PGCGROWTHCONDITIONS
A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
chip antibody: anti-myc PGCGROWTHCONDITIONS
chip antibody cat. #: sc-28207 PGCGROWTHCONDITIONS
chip antibody vendor: Santa Cruz Biotech PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37oC on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4 oC to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4oC to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65oC overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55 oC for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment. PGCGROWTHCONDITIONS
E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
library strategy: ChIP-seq (ChIP-exo) PGCGROWTHCONDITIONS
MACE software (https: PGCGROWTHCONDITIONS
oxyR-8myc-tagged_PQ treated PGCGROWTHCONDITIONS
OxyR PQ 1 PGCGROWTHCONDITIONS
OxyR PQ 2 PGCGROWTHCONDITIONS
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity. PGCGROWTHCONDITIONS
soxR-8myc-tagged_PQ treated PGCGROWTHCONDITIONS
SoxR PQ 1 PGCGROWTHCONDITIONS
SoxR PQ 2 PGCGROWTHCONDITIONS
soxS-8myc-tagged_PQ treated PGCGROWTHCONDITIONS
SoxS PQ 1 PGCGROWTHCONDITIONS
SoxS PQ 2 PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+ PGCGROWTHCONDITIONS
treated with: 250 uM of paraquat at mid-log phase for 20 min PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0 PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA). PGCGROWTHCONDITIONS
treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS
WT PQ PGCGROWTHCONDITIONS
WT PQ 1 PGCGROWTHCONDITIONS
WT PQ 2 PGCGROWTHCONDITIONS
ΔoxyR PQ PGCGROWTHCONDITIONS
ΔoxyR PQ 1 PGCGROWTHCONDITIONS
ΔoxyR PQ 2 PGCGROWTHCONDITIONS
ΔsoxR PQ PGCGROWTHCONDITIONS
ΔsoxR PQ 1 PGCGROWTHCONDITIONS
ΔsoxR PQ 2 PGCGROWTHCONDITIONS
ΔsoxS PQ PGCGROWTHCONDITIONS
ΔsoxS PQ 1 PGCGROWTHCONDITIONS
ΔsoxS PQ 2 PGCGROWTHCONDITIONS
16,000 g for 40 s at room temperature.  The supernatant was discarded, and cell pellets PGCGROWTHCONDITIONS
1.8 ml (ca. 3E+9 cells) were pipetted into 2.0 ml tubes and immediately centrifuged at PGCGROWTHCONDITIONS
68908 PGCGROWTHCONDITIONS
68909 PGCGROWTHCONDITIONS
68910 PGCGROWTHCONDITIONS
68911 PGCGROWTHCONDITIONS
68912 PGCGROWTHCONDITIONS
68913 PGCGROWTHCONDITIONS
68915 PGCGROWTHCONDITIONS
68916 PGCGROWTHCONDITIONS
68917 PGCGROWTHCONDITIONS
68919 PGCGROWTHCONDITIONS
68920 PGCGROWTHCONDITIONS
68921 PGCGROWTHCONDITIONS
68922 PGCGROWTHCONDITIONS
68923 PGCGROWTHCONDITIONS
68924 PGCGROWTHCONDITIONS
68925 PGCGROWTHCONDITIONS
68926 PGCGROWTHCONDITIONS
68927 PGCGROWTHCONDITIONS
68928 PGCGROWTHCONDITIONS
68929 PGCGROWTHCONDITIONS
68930 PGCGROWTHCONDITIONS
68931 PGCGROWTHCONDITIONS
68932 PGCGROWTHCONDITIONS
68933 PGCGROWTHCONDITIONS
Cells were harvested on days 1 and 3 of glucose starvation, with samples taken from the PGCGROWTHCONDITIONS
chilled in a dry ice PGCGROWTHCONDITIONS
D1-ae10 PGCGROWTHCONDITIONS
D1-ae11 PGCGROWTHCONDITIONS
D1-ae12 PGCGROWTHCONDITIONS
D1+ae7 PGCGROWTHCONDITIONS
D1+ae8 PGCGROWTHCONDITIONS
D1+ae9 PGCGROWTHCONDITIONS
D1+AN PGCGROWTHCONDITIONS
D1+AN2 PGCGROWTHCONDITIONS
D1+AN3 PGCGROWTHCONDITIONS
D1-AN4 PGCGROWTHCONDITIONS
D1-AN5 PGCGROWTHCONDITIONS
D1-AN6 PGCGROWTHCONDITIONS
D3+ae19 PGCGROWTHCONDITIONS
D3+ae20 PGCGROWTHCONDITIONS
D3+ae21 PGCGROWTHCONDITIONS
D3-ae22 PGCGROWTHCONDITIONS
D3-ae23 PGCGROWTHCONDITIONS
D3-ae24 PGCGROWTHCONDITIONS
D3+AN13 PGCGROWTHCONDITIONS
D3+AN14 PGCGROWTHCONDITIONS
D3+AN15 PGCGROWTHCONDITIONS
D3-AN16 PGCGROWTHCONDITIONS
D3-AN17 PGCGROWTHCONDITIONS
D3-AN18 PGCGROWTHCONDITIONS
day: . strain: . oxygen: . PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Feature pixel median minus background pixel mean; PGCGROWTHCONDITIONS
further processing PGCGROWTHCONDITIONS
isolated by chloroform extraction and precipitation by isopropanol. Precipitated RNA PGCGROWTHCONDITIONS
normalization subtracting array-median log2 ratio. PGCGROWTHCONDITIONS
pool of aliquots from all samples PGCGROWTHCONDITIONS
ratio set to missing where SNR (feature mean - backround mean  PGCGROWTHCONDITIONS
Reference Pool PGCGROWTHCONDITIONS
re-suspended in 200 ul Trizol and combined for a total volume of 1 ml, then promptly PGCGROWTHCONDITIONS
same cultures used for the viability assay. For each experimental condition, 15 aliquots of PGCGROWTHCONDITIONS
triplicate samples were prepared by combining cells from 5 tubes each.  Each pellet was PGCGROWTHCONDITIONS
was washed with 70 percent ethanol, resuspended in 30 ul water, and held at 4 deg. C for PGCGROWTHCONDITIONS
were immediately frozen in liquid nitrogen and stored at -80 deg. C.  For RNA isolation, PGCGROWTHCONDITIONS
chip antibody: anti-myc (Santa Cruz Biotech, sc-28207) PGCGROWTHCONDITIONS
chip antibody: anti-RpoS (neoclone, WP009) PGCGROWTHCONDITIONS
ChIP-exo GadE pH5.5 1 PGCGROWTHCONDITIONS
ChIP-exo GadE pH5.5 2 PGCGROWTHCONDITIONS
ChIP-exo GadW pH5.5 1 PGCGROWTHCONDITIONS
ChIP-exo GadW pH5.5 2 PGCGROWTHCONDITIONS
ChIP-exo GadX pH5.5 1 PGCGROWTHCONDITIONS
ChIP-exo GadX pH5.5 2 PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S PGCGROWTHCONDITIONS
ChIP-exo RpoS pH5.5 1 PGCGROWTHCONDITIONS
ChIP-exo RpoS pH5.5 2 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: gadE-8myc PGCGROWTHCONDITIONS
genotype: gadW-8myc PGCGROWTHCONDITIONS
genotype: gadX-8myc PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Immunoprecipitated DNA PGCGROWTHCONDITIONS
MACE software (https: PGCGROWTHCONDITIONS
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity. PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+ PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0 PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA). PGCGROWTHCONDITIONS
WT pH5.5 PGCGROWTHCONDITIONS
WT pH5.5 1 PGCGROWTHCONDITIONS
WT pH5.5 2 PGCGROWTHCONDITIONS
ΔgadE pH5.5 PGCGROWTHCONDITIONS
ΔgadE pH5.5 1 PGCGROWTHCONDITIONS
ΔgadE pH5.5 2 PGCGROWTHCONDITIONS
ΔgadW pH5.5 PGCGROWTHCONDITIONS
ΔgadW pH5.5 1 PGCGROWTHCONDITIONS
ΔgadW pH5.5 2 PGCGROWTHCONDITIONS
ΔgadX pH5.5 PGCGROWTHCONDITIONS
ΔgadX pH5.5 1 PGCGROWTHCONDITIONS
ΔgadX pH5.5 2 PGCGROWTHCONDITIONS
Background subtractions and normalization of extracted data were performed through R using the Bioconductor package as described (Yang, Y.H. et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucleic Acid Res 30, e15, 2002; Smyth, G.K. in Bioinformatics and Computational Biology Solutions using R and Bioconductor. 397-420, Springer, New York, 2005). PGCGROWTHCONDITIONS
Cultures of both strains were started with a 2% overnight inoculum in LB media containing 35ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
growth phase: exponential growth phase PGCGROWTHCONDITIONS
growth phase: stationary growth phase PGCGROWTHCONDITIONS
growth phase: transition growth phase PGCGROWTHCONDITIONS
pControl_exponential growth phase_1 ml cell pellet PGCGROWTHCONDITIONS
pControl_stationary growth phase_1 ml cell pellet PGCGROWTHCONDITIONS
pControl_transition growth phase_1 ml cell pellet PGCGROWTHCONDITIONS
plasmid: pControl PGCGROWTHCONDITIONS
plasmid: pLPLσ PGCGROWTHCONDITIONS
pLPLσ_exponential growth phase_1 ml cell pellet PGCGROWTHCONDITIONS
pLPLσ_stationary growth phase_1 ml cell pellet PGCGROWTHCONDITIONS
pLPLσ_transition growth phase_1 ml cell pellet PGCGROWTHCONDITIONS
Replicate 1 - timepoint 1 (4.5h) PGCGROWTHCONDITIONS
Replicate 1 - timepoint 1 (4.5h) - dye swap PGCGROWTHCONDITIONS
Replicate 1 - timepoint 2 (6h) PGCGROWTHCONDITIONS
Replicate 1 - timepoint 2 (6h) - dye swap PGCGROWTHCONDITIONS
Replicate 1 - timepoint 3 (9h) PGCGROWTHCONDITIONS
Replicate 1 - timepoint 3 (9h) - dye swap PGCGROWTHCONDITIONS
Replicate 2 - timepoint 1 (4.5h) PGCGROWTHCONDITIONS
Replicate 2 - timepoint 1 (4.5h) - dye swap PGCGROWTHCONDITIONS
Replicate 2 - timepoint 2 (6h) PGCGROWTHCONDITIONS
Replicate 2 - timepoint 2 (6h) - dye swap PGCGROWTHCONDITIONS
Replicate 2 - timepoint 3 (9h) PGCGROWTHCONDITIONS
Replicate 2 - timepoint 3 (9h) - dye swap PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The optical density was measured every 30 min and expression of the heterologous sigma factor was induced with 1mM IPTG at an optical density of 0.1. Samples for RNA extractions (1ml) were taken after 4.5, 6 and 9 hours after induction. Cell pellets were stored at -80°C until total RNA extraction was performed. PGCGROWTHCONDITIONS
time point: 4.5 hrs after induction PGCGROWTHCONDITIONS
time point: 6 hrs after induction PGCGROWTHCONDITIONS
time point: 9 hrs after induction PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufactures recommendations. PGCGROWTHCONDITIONS
10-HT874-PS-60min1 PGCGROWTHCONDITIONS
11-HT874-PS-60min2 PGCGROWTHCONDITIONS
12-HT874-PS-60min3 PGCGROWTHCONDITIONS
1-HT873-PA1 PGCGROWTHCONDITIONS
1-HT873-PA1- PGCGROWTHCONDITIONS
2-HT873-PA2 PGCGROWTHCONDITIONS
2-HT873-PA2- PGCGROWTHCONDITIONS
3-HT873-PA3 PGCGROWTHCONDITIONS
3-HT873-PA3- PGCGROWTHCONDITIONS
4-HT873-PS-60min1 PGCGROWTHCONDITIONS
5-HT873-PS-60min2 PGCGROWTHCONDITIONS
6-HT873-PS-60min3 PGCGROWTHCONDITIONS
7-HT874-PA1 PGCGROWTHCONDITIONS
7-HT874-PA1- PGCGROWTHCONDITIONS
873-Con1-- PGCGROWTHCONDITIONS
873-Con2-- PGCGROWTHCONDITIONS
873-Con3-- PGCGROWTHCONDITIONS
873-PA1-- PGCGROWTHCONDITIONS
873-PA2-- PGCGROWTHCONDITIONS
873-PA3-- PGCGROWTHCONDITIONS
875-Con1-- PGCGROWTHCONDITIONS
875-Con2-- PGCGROWTHCONDITIONS
875-Con3-- PGCGROWTHCONDITIONS
875-PA1-- PGCGROWTHCONDITIONS
875-PA2-- PGCGROWTHCONDITIONS
875-PA3-- PGCGROWTHCONDITIONS
8-HT874-PA2 PGCGROWTHCONDITIONS
8-HT874-PA2- PGCGROWTHCONDITIONS
9-HT874-PA3 PGCGROWTHCONDITIONS
9-HT874-PA3- PGCGROWTHCONDITIONS
Data was analyzed with RMA using the program Partek 6.6 PGCGROWTHCONDITIONS
E. coli strains HT874, HT873, HT875, HT873 treated with or no polyamines by Trizol protocol. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
HT873-Con1 PGCGROWTHCONDITIONS
HT873-Con2 PGCGROWTHCONDITIONS
HT873-Con3 PGCGROWTHCONDITIONS
HT873-PA1 PGCGROWTHCONDITIONS
HT873-PA2 PGCGROWTHCONDITIONS
HT873-PA3 PGCGROWTHCONDITIONS
HT875-Con1 PGCGROWTHCONDITIONS
HT875-Con2 PGCGROWTHCONDITIONS
HT875-Con3 PGCGROWTHCONDITIONS
HT875-PA1 PGCGROWTHCONDITIONS
HT875-PA2 PGCGROWTHCONDITIONS
HT875-PA3 PGCGROWTHCONDITIONS
RNA were isolated from wild type and mutants. Trizol extraction of total RNA was performed according to standard affymetrix labeling protocols. PGCGROWTHCONDITIONS
strain: HT873 PGCGROWTHCONDITIONS
strain: HT874 PGCGROWTHCONDITIONS
strain: HT875 PGCGROWTHCONDITIONS
treatment: Con1 PGCGROWTHCONDITIONS
treatment: Con2 PGCGROWTHCONDITIONS
treatment: Con3 PGCGROWTHCONDITIONS
treatment: PA1 PGCGROWTHCONDITIONS
treatment: PA2 PGCGROWTHCONDITIONS
treatment: PA3 PGCGROWTHCONDITIONS
treatment: PS-60min PGCGROWTHCONDITIONS
50 ng of the fragmented RNA was converted to sequencing library using TruSeq® Stranded mRNA Sample Prep Kit in accordance with manufacturer’s instruction (Illumina). PGCGROWTHCONDITIONS
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99. PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.4 PGCGROWTHCONDITIONS
cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
From the cells cultured in LB media at 37 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY). PGCGROWTHCONDITIONS
Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media  grown at 37 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 ℃ to mid-exponential phase (OD600 nm ~ 0.6). PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq 37C LB rep1 PGCGROWTHCONDITIONS
RNA-seq 37C LB rep2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM is generated by in-house script PGCGROWTHCONDITIONS
The expression levels were based upon the RPKM metric obtained from strand-specific manner. PGCGROWTHCONDITIONS
Cells were grown in LB at 22°C or 37°C, as indicated. PGCGROWTHCONDITIONS
Cells were resuspended in Lysis buffer (10mM tris, 20% sucrose, 50mM NaCl, 10mM EDTA, 10mg PGCGROWTHCONDITIONS
chip antibody: anti-Flag PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Crosslinking was performed using 1% of forlmaldehyde PGCGROWTHCONDITIONS
deltamatP 22°C PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth temperature: 22°C PGCGROWTHCONDITIONS
growth temperature: 37°C PGCGROWTHCONDITIONS
Illumina Casava v1.8 used for basecalling. PGCGROWTHCONDITIONS
MACS v2.0.10.20131216 was used for peak calling with parameters --llocal=10000 -g 4639675 --bw 300 -p 0.05 --slocal=1000 --keep-dup=20 PGCGROWTHCONDITIONS
MatP 37°C PGCGROWTHCONDITIONS
MukB 22°C PGCGROWTHCONDITIONS
MukB 37°C PGCGROWTHCONDITIONS
MukBDA 22°C PGCGROWTHCONDITIONS
MukB deltamatP 22°C PGCGROWTHCONDITIONS
MukBEQ 22°C PGCGROWTHCONDITIONS
MukBEQ deltamatP 22°C PGCGROWTHCONDITIONS
Reads were adapter removed and trimmed to 40Bp using trimmomatic 0.32 with parameters ILLUMINACLIP: PGCGROWTHCONDITIONS
Sequences were mapped to NC_000913.2 using bowtie2 v2.2.2 with parameters -N 0 --sensitive --minins 130 --maxins 780 -q --no-mixed --no-discordant  --no-unal PGCGROWTHCONDITIONS
Sequencing libraries were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina (#E7370, NEB) for samples 1 to 3 (37 C) and the WaferGen PrepX ILM ChiP-Seq Library Kit (#400075, WaferGen) on the Apollo 324 System for samples 4 to 10 (22 C). PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: MACS v2.0.10.20131216 peaks file PGCGROWTHCONDITIONS
WT 22°C PGCGROWTHCONDITIONS
WT 37°C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g PGCGROWTHCONDITIONS
Exact details for the full computational pipeline are available at https: PGCGROWTHCONDITIONS
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
Glucose time course, 168 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 168 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 168 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 168 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 24 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 24 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 24 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 24 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 336 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 336 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 336 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 336 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 3 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 3 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 3 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 3 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 48 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 48 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 48 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 48 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 4 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 4 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 4 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 4 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 5 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 5 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 5 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 5 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 6 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 6 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 6 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 6 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Glucose time course, 8 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Glucose time course, 8 hour time point, biological replicate 2 PGCGROWTHCONDITIONS
Glucose time course, 8 hourt ime point, biological replicate 3 PGCGROWTHCONDITIONS
Glucose time course, 8 hourt ime point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
molecule subtype: rRNA-depleted total RNA PGCGROWTHCONDITIONS
molecule subtype: total RNA PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_168 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_168 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_24 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_24 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_336 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_336 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_3 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_3 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_48 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_48 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_4 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_4 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_5 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_5 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_6 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_6 hr_rRNA not depleted PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_8 hr PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_8 hr_rRNA not depleted PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap PGCGROWTHCONDITIONS
RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre) PGCGROWTHCONDITIONS
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
strain: REL606 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
time point: 168 hours PGCGROWTHCONDITIONS
time point: 24 hours PGCGROWTHCONDITIONS
time point: 336 hours PGCGROWTHCONDITIONS
time point: 3 hours PGCGROWTHCONDITIONS
time point: 48 hours PGCGROWTHCONDITIONS
time point: 4 hours PGCGROWTHCONDITIONS
time point: 5 hours PGCGROWTHCONDITIONS
time point: 6 hours PGCGROWTHCONDITIONS
time point: 8 hours PGCGROWTHCONDITIONS
Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
After normalization, the expression of a gene was calculated by a RMA-summarization procedure within each growth condition. PGCGROWTHCONDITIONS
agno3 concentration in µm: 0 PGCGROWTHCONDITIONS
agno3 concentration in µm: 5 PGCGROWTHCONDITIONS
agno3 concentration in µm: 6.5 PGCGROWTHCONDITIONS
agno3 concentration in µm: 8.5 PGCGROWTHCONDITIONS
At 3 h of culture, 60 mL of culture (at OD595 nm = 0.73 ± 0.07, 0.63 ± 0.02, 0.12 ± 0.01 and 0.11 ± 0.02 for cultures subjected to 0, 5.0, 6.5 and 8.5 µM AgNO3, respectively) were sampled and centrifuged (4000 rpm, 5 min, 4 °C), then the pellet was frozen in liquid nitrogen. The pellet was resuspended with 1 mL of TE buffer (Tris-HCl 10 mM, pH 8, EDTA 1 mM, 1 mg lysozyme) and incubated 5 min at room temperature. Total RNA was extracted with a RNeasy midi kit (Qiagen), including the DNase I treatment described in the manufacturer’s instructions. Total RNA quantity and integrity were checked by Nanodrop® and Agilent BioAnalyzer, respectively. PGCGROWTHCONDITIONS
Ecoli_Ag0.0_rep1 PGCGROWTHCONDITIONS
Ecoli_Ag0.0_rep2 PGCGROWTHCONDITIONS
Ecoli_Ag0.0_rep3 PGCGROWTHCONDITIONS
Ecoli_Ag5.0_rep1 PGCGROWTHCONDITIONS
Ecoli_Ag5.0_rep2 PGCGROWTHCONDITIONS
Ecoli_Ag5.0_rep3 PGCGROWTHCONDITIONS
Ecoli_Ag6.5_rep1 PGCGROWTHCONDITIONS
Ecoli_Ag6.5_rep2 PGCGROWTHCONDITIONS
Ecoli_Ag6.5_rep3 PGCGROWTHCONDITIONS
Ecoli_Ag8.5_rep1 PGCGROWTHCONDITIONS
Ecoli_Ag8.5_rep2 PGCGROWTHCONDITIONS
Ecoli_Ag8.5_rep3 PGCGROWTHCONDITIONS
Escherichia coli,  0 µM AgNO3 PGCGROWTHCONDITIONS
Escherichia coli, 0 µM AgNO3 PGCGROWTHCONDITIONS
Escherichia coli, 5 µM AgNO3 PGCGROWTHCONDITIONS
Escherichia coli, 6.5 µM AgNO3 PGCGROWTHCONDITIONS
Escherichia coli, 8.5 µM AgNO3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Ionic silver stock solutions were prepared from AgNO3 powder (Fisher Scientific Bioblock) as previously described (Saulou, Jamme et al., 2013) and stored in darkness. The final tested concentrations (5.0, 6.5, and 8.5 µM) were obtained by diluting the corresponding AgNO3 stock solution directly into the M9 growth medium. Control experiment was simultaneously performed by adding deionised water into the M9 broth. In both cases, a stabilization period of 24 h (at 37 °C and 120 rpm) was carried out before cell inoculation. PGCGROWTHCONDITIONS
Raw probe intensities ( .pair files three replicates for each growth condition with respectively 0, 5.0, 6.5 and 8.5 µM of AgNO3 in the medium) was processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Raw data were submitted to a RMA-base background correction [Irizarry et al, 2003, Biostatistics 4(2): 249-264]. After background correction, intra-replicate quantil normalization was performed for each growth condition. A set of probes in the background for which the ranks were roughly invariant across all the twelve arrays was selected. The median value of the invariant probeset intensities on each array was used as a scaling factor for normalization between growth conditions. PGCGROWTHCONDITIONS
The laboratory strain E. coli K12 MG1655 was grown for 24 h at 37 °C under continuous shaking (120 rpm), in 200 mL M9 medium (Merck Prolabo) complemented with 2.5 g PGCGROWTHCONDITIONS
15 ml of culture was mixed with 30 ml of RNAprotect bacterial reagent (QIAGEN Ltd). PGCGROWTHCONDITIONS
An RNeasy midikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd). PGCGROWTHCONDITIONS
Data was analysed using GeneSpring PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Growth: Anaerobic to early exponential growth PGCGROWTHCONDITIONS
Media:Minimal salts + 20 mM trimethylamine-N-oxide PGCGROWTHCONDITIONS
Media:Minimal salts + 20 mM trimethylamine-N-oxide +2.5 mM sodium nitrite PGCGROWTHCONDITIONS
pGIT1 PGCGROWTHCONDITIONS
pGIT1.1 PGCGROWTHCONDITIONS
pGIT1.1 + NO2 PGCGROWTHCONDITIONS
pGIT1.2 PGCGROWTHCONDITIONS
pGIT1.2 + NO2 PGCGROWTHCONDITIONS
pGIT1.3 PGCGROWTHCONDITIONS
pGIT1.3 + NO2 PGCGROWTHCONDITIONS
pGIT1.4 PGCGROWTHCONDITIONS
pGIT1.4 + NO2 PGCGROWTHCONDITIONS
pGIT1 + NO2 PGCGROWTHCONDITIONS
pGIT8 PGCGROWTHCONDITIONS
pGIT8.1 + NO2 PGCGROWTHCONDITIONS
pGIT8.2 + NO2 PGCGROWTHCONDITIONS
pGIT8.3 + NO2 PGCGROWTHCONDITIONS
pGIT8.4 + NO2 PGCGROWTHCONDITIONS
pGIT8 + NO2 PGCGROWTHCONDITIONS
Pool of eight independent cultures PGCGROWTHCONDITIONS
Strain: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation) PGCGROWTHCONDITIONS
Strain: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide PGCGROWTHCONDITIONS
Strain: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide  PGCGROWTHCONDITIONS
Strain: MG1655 pGIT1 (carries the ytfE promoter in multicopy, titrates out NsrR to phenocopy an NsrR- mutation) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide +2.5 mM sodium nitrite PGCGROWTHCONDITIONS
Strain: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) PGCGROWTHCONDITIONS
Strain: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide + 2.5 mM sodium nitrite PGCGROWTHCONDITIONS
Strain: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide +2.5 mM sodium nitrite PGCGROWTHCONDITIONS
Strain: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide + .5 mM sodium nitrite PGCGROWTHCONDITIONS
Strain: MG1655 pGIT8 (carries 1 base pair deletion in the NsrR-binding site of the ytfE promoter) Growth: Anaerobic to early exponential growth Media:Minimal salts + 20 mM trimethylamine-N-oxide Pool of eight independent cultures PGCGROWTHCONDITIONS
b2618_U_N0075_r1 PGCGROWTHCONDITIONS
b2618_U_N0075_r2 PGCGROWTHCONDITIONS
b2618_U_N0075_r3 PGCGROWTHCONDITIONS
b2618 upregulation, 0.075 ug PGCGROWTHCONDITIONS
bcp___U_N0075_r1 PGCGROWTHCONDITIONS
bcp___U_N0075_r2 PGCGROWTHCONDITIONS
bcp___U_N0075_r3 PGCGROWTHCONDITIONS
bcp upregulation, 0.075 ug PGCGROWTHCONDITIONS
ccdB_K12_0_r1 PGCGROWTHCONDITIONS
ccdB_K12_120_r1 PGCGROWTHCONDITIONS
ccdB_K12_30_r1 PGCGROWTHCONDITIONS
ccdB_K12_60_r1 PGCGROWTHCONDITIONS
ccdB_K12_90_r1 PGCGROWTHCONDITIONS
ccdB_MG1063_0_r1 PGCGROWTHCONDITIONS
ccdB_MG1063_0_r2 PGCGROWTHCONDITIONS
ccdB_MG1063_120_r1 PGCGROWTHCONDITIONS
ccdB_MG1063_30_r1 PGCGROWTHCONDITIONS
ccdB_MG1063_30_r2 PGCGROWTHCONDITIONS
ccdB_MG1063_60_r1 PGCGROWTHCONDITIONS
ccdB_MG1063_60_r2 PGCGROWTHCONDITIONS
ccdB_MG1063_90_r1 PGCGROWTHCONDITIONS
ccdB_MG1063_90_r2 PGCGROWTHCONDITIONS
ccdB_W1863_0_r1 PGCGROWTHCONDITIONS
ccdB_W1863_30_r1 PGCGROWTHCONDITIONS
ccdB_W1863_60_r1 PGCGROWTHCONDITIONS
ccdB_W1863_90_r1 PGCGROWTHCONDITIONS
cells 12 min after treatment by norfloxacin PGCGROWTHCONDITIONS
cells 24 min after treatment by norfloxacin PGCGROWTHCONDITIONS
cells 36 min after treatment by norfloxacin PGCGROWTHCONDITIONS
cells 48 min after treatment by norfloxacin PGCGROWTHCONDITIONS
cells 60 min after treatment by norfloxacin PGCGROWTHCONDITIONS
cells prior to treatment by norfloxacin PGCGROWTHCONDITIONS
cpxR__U_N0075_r1 PGCGROWTHCONDITIONS
cpxR__U_N0075_r2 PGCGROWTHCONDITIONS
cpxR__U_N0075_r3 PGCGROWTHCONDITIONS
cpxR upregulation, 0.075 ug PGCGROWTHCONDITIONS
crcB__U_N0075_r1 PGCGROWTHCONDITIONS
crcB__U_N0075_r2 PGCGROWTHCONDITIONS
crcB__U_N0075_r3 PGCGROWTHCONDITIONS
crcB upregulation, 0.075 ug PGCGROWTHCONDITIONS
crp___U_N0075_r1 PGCGROWTHCONDITIONS
crp___U_N0075_r2 PGCGROWTHCONDITIONS
crp___U_N0075_r3 PGCGROWTHCONDITIONS
crp upregulation, 0.075 ug PGCGROWTHCONDITIONS
cspF__U_N0075_r1 PGCGROWTHCONDITIONS
cspF__U_N0075_r2 PGCGROWTHCONDITIONS
cspF__U_N0075_r3 PGCGROWTHCONDITIONS
cspF upregulation, 0.075 ug PGCGROWTHCONDITIONS
dam___U_N0075_r1 PGCGROWTHCONDITIONS
dam___U_N0075_r2 PGCGROWTHCONDITIONS
dam___U_N0075_r3 PGCGROWTHCONDITIONS
dam upregulation, 0.075 ug PGCGROWTHCONDITIONS
dinI___U_N0025_r1 PGCGROWTHCONDITIONS
dinI___U_N0025_r2 PGCGROWTHCONDITIONS
dinI___U_N0025_r3 PGCGROWTHCONDITIONS
dinI upregulation, amp 50ug PGCGROWTHCONDITIONS
dinP___U_N0025_r1 PGCGROWTHCONDITIONS
dinP___U_N0025_r2 PGCGROWTHCONDITIONS
dinP___U_N0025_r3 PGCGROWTHCONDITIONS
dinP upregulation, amp 50ug PGCGROWTHCONDITIONS
dnaA__U_N0075_r1 PGCGROWTHCONDITIONS
dnaA__U_N0075_r2 PGCGROWTHCONDITIONS
dnaA__U_N0075_r3 PGCGROWTHCONDITIONS
dnaA upregulation, 0.075 ug PGCGROWTHCONDITIONS
dnaN__U_N0075_r1 PGCGROWTHCONDITIONS
dnaN__U_N0075_r2 PGCGROWTHCONDITIONS
dnaN__U_N0075_r3 PGCGROWTHCONDITIONS
dnaN upregulation, 0.075 ug PGCGROWTHCONDITIONS
dnaT__U_N0075_r1 PGCGROWTHCONDITIONS
dnaT__U_N0075_r2 PGCGROWTHCONDITIONS
dnaT__U_N0075_r3 PGCGROWTHCONDITIONS
dnaT upregulation, 0.075 ug PGCGROWTHCONDITIONS
E.coli K12 with ccdB upregulation 0 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with ccdB upregulation 120 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with ccdB upregulation 30 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with ccdB upregulation 60 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with ccdB upregulation 90 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with lacZ upregulation 0 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with lacZ upregulation 120 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with lacZ upregulation 30 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with lacZ upregulation 60 minutes after induction PGCGROWTHCONDITIONS
E.coli K12 with lacZ upregulation 90 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with ccdB upregulation 0 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with ccdB upregulation 120 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with ccdB upregulation 30 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with ccdB upregulation 60 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with ccdB upregulation 90 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with lacZ upregulation 0 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with lacZ upregulation 120 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with lacZ upregulation 30 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with lacZ upregulation 60 minutes after induction PGCGROWTHCONDITIONS
E.coli MG1063 (recA56 = recA-) with lacZ upregulation 90 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with ccdB upregulation 0 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with ccdB upregulation 30 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with ccdB upregulation 60 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with ccdB upregulation 90 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with lacZ upregulation 0 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with lacZ upregulation 30 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with lacZ upregulation 60 minutes after induction PGCGROWTHCONDITIONS
E.coli W1863 wt lambda- with lacZ upregulation 90 minutes after induction PGCGROWTHCONDITIONS
emrR__U_N0075_r1 PGCGROWTHCONDITIONS
emrR__U_N0075_r3 PGCGROWTHCONDITIONS
emrR upregulation, 0.075 ug PGCGROWTHCONDITIONS
era___U_N0075_r1 PGCGROWTHCONDITIONS
era___U_N0075_r2 PGCGROWTHCONDITIONS
era___U_N0075_r3 PGCGROWTHCONDITIONS
era upregulation, 0.075 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
fis___U_N0075_r1 PGCGROWTHCONDITIONS
fis___U_N0075_r2 PGCGROWTHCONDITIONS
fis___U_N0075_r3 PGCGROWTHCONDITIONS
fis upregulation, 0.075 ug PGCGROWTHCONDITIONS
fklB__U_N0075_r1 PGCGROWTHCONDITIONS
fklB__U_N0075_r2 PGCGROWTHCONDITIONS
fklB__U_N0075_r3 PGCGROWTHCONDITIONS
fklB upregulation, 0.075 ug PGCGROWTHCONDITIONS
folA__U_N0075_r1 PGCGROWTHCONDITIONS
folA__U_N0075_r2 PGCGROWTHCONDITIONS
folA__U_N0075_r3 PGCGROWTHCONDITIONS
folA upregulation, 0.075 ug PGCGROWTHCONDITIONS
galF__U_N0075_r1 PGCGROWTHCONDITIONS
galF__U_N0075_r2 PGCGROWTHCONDITIONS
galF__U_N0075_r3 PGCGROWTHCONDITIONS
galF upregulation, 0.075 ug PGCGROWTHCONDITIONS
gcvR__U_N0075_r1 PGCGROWTHCONDITIONS
gcvR__U_N0075_r2 PGCGROWTHCONDITIONS
gcvR__U_N0075_r3 PGCGROWTHCONDITIONS
gcvR upregulation, 0.075 mg PGCGROWTHCONDITIONS
GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000 PGCGROWTHCONDITIONS
gyrA__U_N0075_r1 PGCGROWTHCONDITIONS
gyrA__U_N0075_r2 PGCGROWTHCONDITIONS
gyrA__U_N0075_r3 PGCGROWTHCONDITIONS
gyrA upregulation, 0.075 mg PGCGROWTHCONDITIONS
gyrI__U_N0075_r1 PGCGROWTHCONDITIONS
gyrI__U_N0075_r2 PGCGROWTHCONDITIONS
gyrI__U_N0075_r3 PGCGROWTHCONDITIONS
gyrI upregulation, 0.075 mg PGCGROWTHCONDITIONS
hlpA__U_N0075_r1 PGCGROWTHCONDITIONS
hlpA__U_N0075_r2 PGCGROWTHCONDITIONS
hlpA__U_N0075_r3 PGCGROWTHCONDITIONS
hlpA upregulation, 0.075 mg PGCGROWTHCONDITIONS
holD__U_N0075_r1 PGCGROWTHCONDITIONS
holD__U_N0075_r2 PGCGROWTHCONDITIONS
holD__U_N0075_r3 PGCGROWTHCONDITIONS
holD upregulation, 0.075 mg PGCGROWTHCONDITIONS
hscA__U_N0075_r1 PGCGROWTHCONDITIONS
hscA__U_N0075_r2 PGCGROWTHCONDITIONS
hscA__U_N0075_r3 PGCGROWTHCONDITIONS
hscA upregulation, 0.075 mg PGCGROWTHCONDITIONS
IHF___U_N0075_r1 PGCGROWTHCONDITIONS
IHF___U_N0075_r3 PGCGROWTHCONDITIONS
IHF upregulation, 0.075 mg PGCGROWTHCONDITIONS
ik_H2_T2.5_r1 PGCGROWTHCONDITIONS
ik_H2_T3.5_r1 PGCGROWTHCONDITIONS
ik_H2_T3_r1 PGCGROWTHCONDITIONS
ik_H2_T4.5_r1 PGCGROWTHCONDITIONS
ik_H2_T4_r1 PGCGROWTHCONDITIONS
ik_H2_T5.5_r1 PGCGROWTHCONDITIONS
ik_H2_T5_r1 PGCGROWTHCONDITIONS
ik_H2_T6_r1 PGCGROWTHCONDITIONS
ik_H2_T8_r1 PGCGROWTHCONDITIONS
ik_L2_T2.5_r1 PGCGROWTHCONDITIONS
ik_L2_T3.5_r1 PGCGROWTHCONDITIONS
ik_L2_T3_r1 PGCGROWTHCONDITIONS
ik_L2_T4.5_r1 PGCGROWTHCONDITIONS
ik_L2_T4_r1 PGCGROWTHCONDITIONS
ik_L2_T5.5_r1 PGCGROWTHCONDITIONS
ik_L2_T5_r1 PGCGROWTHCONDITIONS
ik_L2_T6_r1 PGCGROWTHCONDITIONS
ik_L2_T8_r1 PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 2.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 3.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 3 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 4.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 4 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 5.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 6 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.2 percent glucose, 8 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 2.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 3.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 3 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 4.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 4 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 5.5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 5 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 6 hours post-incubation PGCGROWTHCONDITIONS
K12 EMG2 on LB with 0.4 percent glucose, 8 hours post-incubation PGCGROWTHCONDITIONS
lacZ_K12_0_r1 PGCGROWTHCONDITIONS
lacZ_K12_120_r1 PGCGROWTHCONDITIONS
lacZ_K12_30_r1 PGCGROWTHCONDITIONS
lacZ_K12_60_r1 PGCGROWTHCONDITIONS
lacZ_K12_90_r1 PGCGROWTHCONDITIONS
lacZ_MG1063_0_r1 PGCGROWTHCONDITIONS
lacZ_MG1063_0_r2 PGCGROWTHCONDITIONS
lacZ_MG1063_120_r1 PGCGROWTHCONDITIONS
lacZ_MG1063_30_r1 PGCGROWTHCONDITIONS
lacZ_MG1063_30_r2 PGCGROWTHCONDITIONS
lacZ_MG1063_60_r1 PGCGROWTHCONDITIONS
lacZ_MG1063_60_r2 PGCGROWTHCONDITIONS
lacZ_MG1063_90_r1 PGCGROWTHCONDITIONS
lacZ_MG1063_90_r2 PGCGROWTHCONDITIONS
lacZ_W1863_0_r1 PGCGROWTHCONDITIONS
lacZ_W1863_30_r1 PGCGROWTHCONDITIONS
lacZ_W1863_60_r1 PGCGROWTHCONDITIONS
lacZ_W1863_90_r1 PGCGROWTHCONDITIONS
ldrA__U_N0075_r1 PGCGROWTHCONDITIONS
ldrA__U_N0075_r2 PGCGROWTHCONDITIONS
ldrA__U_N0075_r3 PGCGROWTHCONDITIONS
ldrA upregulation, 0.075 mg PGCGROWTHCONDITIONS
lexA___U_N0025_r1 PGCGROWTHCONDITIONS
lexA___U_N0025_r2 PGCGROWTHCONDITIONS
lexA___U_N0025_r3 PGCGROWTHCONDITIONS
lexA upregulation, amp 50ug PGCGROWTHCONDITIONS
lon___U_N0025_r1 PGCGROWTHCONDITIONS
lon___U_N0025_r2 PGCGROWTHCONDITIONS
lon___U_N0025_r3 PGCGROWTHCONDITIONS
lon upregulation, amp 50ug PGCGROWTHCONDITIONS
luc2_U_N0000_r1 PGCGROWTHCONDITIONS
luc2_U_N0000_r2 PGCGROWTHCONDITIONS
luc2_U_N0025_r1 PGCGROWTHCONDITIONS
luc2_U_N0025_r2 PGCGROWTHCONDITIONS
luciferase 0.025ug PGCGROWTHCONDITIONS
luciferase no drug PGCGROWTHCONDITIONS
luc___U_N0000_r1 PGCGROWTHCONDITIONS
luc___U_N0000_r2 PGCGROWTHCONDITIONS
luc___U_N0000_r3 PGCGROWTHCONDITIONS
luc___U_N0025_r1 PGCGROWTHCONDITIONS
luc___U_N0025_r2 PGCGROWTHCONDITIONS
luc___U_N0025_r3 PGCGROWTHCONDITIONS
luc___U_N0075_r1 PGCGROWTHCONDITIONS
luc___U_N0075_r2 PGCGROWTHCONDITIONS
luc___U_N0075_r3 PGCGROWTHCONDITIONS
luc upregulation, 0.000 ug PGCGROWTHCONDITIONS
luc upregulation, 0.075ug PGCGROWTHCONDITIONS
luc upregulation, amp 50ug PGCGROWTHCONDITIONS
mazF_chpA upregulation, amp 50ug PGCGROWTHCONDITIONS
mazF___U_N0025_r1 PGCGROWTHCONDITIONS
mazF___U_N0025_r2 PGCGROWTHCONDITIONS
mazF___U_N0025_r3 PGCGROWTHCONDITIONS
mcrB__U_N0075_r1 PGCGROWTHCONDITIONS
mcrB__U_N0075_r2 PGCGROWTHCONDITIONS
mcrB__U_N0075_r3 PGCGROWTHCONDITIONS
mcrB upregulation, 0.075 mg PGCGROWTHCONDITIONS
mcrC__U_N0075_r1 PGCGROWTHCONDITIONS
mcrC__U_N0075_r2 PGCGROWTHCONDITIONS
mcrC__U_N0075_r3 PGCGROWTHCONDITIONS
mcrC upregulation, 0.075 mg PGCGROWTHCONDITIONS
menB__U_N0075_r1 PGCGROWTHCONDITIONS
menB__U_N0075_r2 PGCGROWTHCONDITIONS
menB__U_N0075_r3 PGCGROWTHCONDITIONS
menB upregulation, 0.075 mg PGCGROWTHCONDITIONS
menC__U_N0075_r1 PGCGROWTHCONDITIONS
menC__U_N0075_r2 PGCGROWTHCONDITIONS
menC__U_N0075_r3 PGCGROWTHCONDITIONS
menC upregulation, 0.075 mg PGCGROWTHCONDITIONS
minD__U_N0075_r1 PGCGROWTHCONDITIONS
minD__U_N0075_r2 PGCGROWTHCONDITIONS
minD__U_N0075_r3 PGCGROWTHCONDITIONS
minD upregulation, 0.075 mg PGCGROWTHCONDITIONS
minE__U_N0075_r1 PGCGROWTHCONDITIONS
minE__U_N0075_r2 PGCGROWTHCONDITIONS
minE__U_N0075_r3 PGCGROWTHCONDITIONS
minE upregulation, 0.075 mg PGCGROWTHCONDITIONS
murI__U_N0075_r1 PGCGROWTHCONDITIONS
murI__U_N0075_r2 PGCGROWTHCONDITIONS
murI__U_N0075_r3 PGCGROWTHCONDITIONS
murI upregulation, 0.075 mg PGCGROWTHCONDITIONS
nrdA__U_N0075_r1 PGCGROWTHCONDITIONS
nrdA__U_N0075_r2 PGCGROWTHCONDITIONS
nrdA__U_N0075_r3 PGCGROWTHCONDITIONS
nrdA upregulation, 0.075 mg PGCGROWTHCONDITIONS
nrdB__U_N0075_r1 PGCGROWTHCONDITIONS
nrdB__U_N0075_r3 PGCGROWTHCONDITIONS
nrdB upregulation, 0.075 mg PGCGROWTHCONDITIONS
nupC__U_N0075_r1 PGCGROWTHCONDITIONS
nupC__U_N0075_r2 PGCGROWTHCONDITIONS
nupC__U_N0075_r3 PGCGROWTHCONDITIONS
nupC upregulation, 0.075 mg PGCGROWTHCONDITIONS
pyrC__U_N0075_r1 PGCGROWTHCONDITIONS
pyrC__U_N0075_r2 PGCGROWTHCONDITIONS
pyrC__U_N0075_r3 PGCGROWTHCONDITIONS
pyrC upregulation, 0.075 mg PGCGROWTHCONDITIONS
recA deletion 0.05 ug PGCGROWTHCONDITIONS
recA deletion 0 ug PGCGROWTHCONDITIONS
recA deletion 1.0 ug PGCGROWTHCONDITIONS
recA_D_N0000_r1 PGCGROWTHCONDITIONS
recA_D_N0000_r2 PGCGROWTHCONDITIONS
recA_D_N0050_r1 PGCGROWTHCONDITIONS
recA_D_N0050_r2 PGCGROWTHCONDITIONS
recA_D_N1000_r1 PGCGROWTHCONDITIONS
recA_D_N1000_r2 PGCGROWTHCONDITIONS
recA___U_N0025_r1 PGCGROWTHCONDITIONS
recA___U_N0025_r2 PGCGROWTHCONDITIONS
recA___U_N0025_r3 PGCGROWTHCONDITIONS
recA upregulation, amp 50ug PGCGROWTHCONDITIONS
relE___U_N0025_r1 PGCGROWTHCONDITIONS
relE___U_N0025_r2 PGCGROWTHCONDITIONS
relE___U_N0025_r3 PGCGROWTHCONDITIONS
relE upregulation, amp 50ug PGCGROWTHCONDITIONS
rimI__U_N0075_r1 PGCGROWTHCONDITIONS
rimI__U_N0075_r2 PGCGROWTHCONDITIONS
rimI__U_N0075_r3 PGCGROWTHCONDITIONS
rimI upregulation, 0.075 mg PGCGROWTHCONDITIONS
RNAEasy with RNAProtect(Qiagen) PGCGROWTHCONDITIONS
rstB__U_N0075_r1 PGCGROWTHCONDITIONS
rstB__U_N0075_r2 PGCGROWTHCONDITIONS
rstB__U_N0075_r3 PGCGROWTHCONDITIONS
rstB upregulation, 0.075 mg PGCGROWTHCONDITIONS
ruvA___U_N0025_r1 PGCGROWTHCONDITIONS
ruvA___U_N0025_r2 PGCGROWTHCONDITIONS
ruvA___U_N0025_r3 PGCGROWTHCONDITIONS
ruvA upregulation, amp 50ug PGCGROWTHCONDITIONS
ruvC__U_N0075_r1 PGCGROWTHCONDITIONS
ruvC__U_N0075_r2 PGCGROWTHCONDITIONS
ruvC__U_N0075_r3 PGCGROWTHCONDITIONS
ruvC upregulation, 0.075 mg PGCGROWTHCONDITIONS
sbcB__U_N0075_r1 PGCGROWTHCONDITIONS
sbcB__U_N0075_r2 PGCGROWTHCONDITIONS
sbcB__U_N0075_r3 PGCGROWTHCONDITIONS
sbcB upregulation, 0.075 mg PGCGROWTHCONDITIONS
sulA___U_N0025_r1 PGCGROWTHCONDITIONS
sulA___U_N0025_r2 PGCGROWTHCONDITIONS
sulA___U_N0025_r3 PGCGROWTHCONDITIONS
sulA upregulation, amp 50ug PGCGROWTHCONDITIONS
T0_N0025_r1 PGCGROWTHCONDITIONS
T0_N0025_r2 PGCGROWTHCONDITIONS
T0_N0025_r3 PGCGROWTHCONDITIONS
T12_N0025_r1 PGCGROWTHCONDITIONS
T12_N0025_r2 PGCGROWTHCONDITIONS
T12_N0025_r3 PGCGROWTHCONDITIONS
T24_N0000_r1 PGCGROWTHCONDITIONS
T24_N0000_r2 PGCGROWTHCONDITIONS
T24_N0000_r3 PGCGROWTHCONDITIONS
T24_N0025_r1 PGCGROWTHCONDITIONS
T24_N0025_r2 PGCGROWTHCONDITIONS
T24_N0025_r3 PGCGROWTHCONDITIONS
T36_N0025_r1 PGCGROWTHCONDITIONS
T36_N0025_r2 PGCGROWTHCONDITIONS
T36_N0025_r3 PGCGROWTHCONDITIONS
T48_N0025_r1 PGCGROWTHCONDITIONS
T48_N0025_r2 PGCGROWTHCONDITIONS
T48_N0025_r3 PGCGROWTHCONDITIONS
T60_N0000_r1 PGCGROWTHCONDITIONS
T60_N0000_r2 PGCGROWTHCONDITIONS
T60_N0000_r3 PGCGROWTHCONDITIONS
T60_N0025_r1 PGCGROWTHCONDITIONS
T60_N0025_r2 PGCGROWTHCONDITIONS
T60_N0025_r3 PGCGROWTHCONDITIONS
umuD___U_N0025_r1 PGCGROWTHCONDITIONS
umuD___U_N0025_r2 PGCGROWTHCONDITIONS
umuD___U_N0025_r3 PGCGROWTHCONDITIONS
umuD upregulation, amp 50ug PGCGROWTHCONDITIONS
untreated cells after 24 min PGCGROWTHCONDITIONS
untreated cells after 60 min PGCGROWTHCONDITIONS
uspA__U_N0075_r1 PGCGROWTHCONDITIONS
uspA__U_N0075_r2 PGCGROWTHCONDITIONS
uspA__U_N0075_r3 PGCGROWTHCONDITIONS
uspA upregulation, 0.075 mg PGCGROWTHCONDITIONS
uvrA___U_N0025_r1 PGCGROWTHCONDITIONS
uvrA___U_N0025_r2 PGCGROWTHCONDITIONS
uvrA___U_N0025_r3 PGCGROWTHCONDITIONS
uvrA upregulation, amp 50ug PGCGROWTHCONDITIONS
wild-type 1.0 ug PGCGROWTHCONDITIONS
wild-type cells with 0.025 ug PGCGROWTHCONDITIONS
wild-type cells with 0.050 ug PGCGROWTHCONDITIONS
wild-type cells with 0.075 ug PGCGROWTHCONDITIONS
wild-type cells without norfloxacin PGCGROWTHCONDITIONS
WT_D_N1000_r1 PGCGROWTHCONDITIONS
WT_D_N1000_r2 PGCGROWTHCONDITIONS
WT_N0000_r1 PGCGROWTHCONDITIONS
WT_N0000_r2 PGCGROWTHCONDITIONS
WT_N0025_r1 PGCGROWTHCONDITIONS
WT_N0025_r2 PGCGROWTHCONDITIONS
WT_N0050_r1 PGCGROWTHCONDITIONS
WT_N0050_r2 PGCGROWTHCONDITIONS
WT_N0075_r1 PGCGROWTHCONDITIONS
WT_N0075_r2 PGCGROWTHCONDITIONS
yebF__U_N0075_r1 PGCGROWTHCONDITIONS
yebF__U_N0075_r2 PGCGROWTHCONDITIONS
yebF__U_N0075_r3 PGCGROWTHCONDITIONS
yebF upregulation, 0.075ug PGCGROWTHCONDITIONS
yoeB__U_N0075_r1 PGCGROWTHCONDITIONS
yoeB__U_N0075_r2 PGCGROWTHCONDITIONS
yoeB__U_N0075_r3 PGCGROWTHCONDITIONS
yoeB upregulation, 0.075 mg PGCGROWTHCONDITIONS
zipA__U_N0075_r1 PGCGROWTHCONDITIONS
zipA__U_N0075_r2 PGCGROWTHCONDITIONS
zipA__U_N0075_r3 PGCGROWTHCONDITIONS
zipA upregulation, 0.075ug PGCGROWTHCONDITIONS
BW25113 W PGCGROWTHCONDITIONS
BW25113 ymgB LBglu 24h biofilm cells PGCGROWTHCONDITIONS
channel 1 PGCGROWTHCONDITIONS
Channel 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of BW25113 wild type after 24h of growth in LBglu with glass wool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of BW25113 ymgB mutant after 24h of growth in LBglu with glass wool PGCGROWTHCONDITIONS
To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia PGCGROWTHCONDITIONS
agent: control PGCGROWTHCONDITIONS
agent: glycolaldehyde PGCGROWTHCONDITIONS
Data were analyzed by Feature Extraction V.11.5.1.1. RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
M9 mineral medium containing (D)-xylose as the only carbon source (100 ml in 500 ml shake flasks) was inoculated from exponentially growing wild-type cells or synthetic cells (cultivated on xylose M9 medium) to adjust an OD of ~0.1. Cultures were incubated at 37°C under shaking until OD reached ~1. Then they were split into two 50 ml aliquots and further cultivated in 250 ml shake flasks in the presence or absence of 10 mM glycolaldehyde. After 30 min of incubation, 1 ml of the cell suspension was withdrawn and centrifuged at 1500 x g (Eppendorf 5415D) for 5 min. The supernatant was removed and the cell pellets were directly subject to RNA extraction. Experiment were repeated three times. PGCGROWTHCONDITIONS
PEN205 PGCGROWTHCONDITIONS
PEN205 strain first repetition PGCGROWTHCONDITIONS
PEN205 strain second repetition PGCGROWTHCONDITIONS
PEN205 strain third repetition PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The RNeasy Mini Kit (QIAGEN) was used to extract RNA. Quantity and quality of the samples were determined by NanoDrop (Thermo) and Bioanalyzer (Agilent Technologies), respectively PGCGROWTHCONDITIONS
wild-type MG1655 PGCGROWTHCONDITIONS
wild-type MG1655 + glycolaldehyde 10 mM PGCGROWTHCONDITIONS
WT cells were treated with 10 mM Glycolaldehyde for 30 min whenever the culture OD600nm reached ~1. PGCGROWTHCONDITIONS
WT strain treated with glycolaldehyde first repetition PGCGROWTHCONDITIONS
WT strain treated with glycolaldehyde second repetition PGCGROWTHCONDITIONS
WT strain treated with glycolaldehyde third repetition PGCGROWTHCONDITIONS
WT strain without glycolaldehyde first repetition PGCGROWTHCONDITIONS
WT strain without glycolaldehyde second repetition PGCGROWTHCONDITIONS
WT strain without glycolaldehyde third repetition PGCGROWTHCONDITIONS
Cells were disrupted by sonication and NsrR bound DNA was isolated with anti-Flag antibody. PGCGROWTHCONDITIONS
chip antibody: Monoclonal ANTI-FLAG  M5(Sigma-Aldrich, catalog number: F4042 ) PGCGROWTHCONDITIONS
chip antibody: none PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq reads were aligned to the CFT073 genome using bowtie (version 0.12.8) PGCGROWTHCONDITIONS
DNA fragments were treated with Epicentre End-It DNA End Repair Kit and 3’ A overhangs were added with DNA polymerase I (Klenow fragment).  Adapters from the IlluminaTruSeq DNA sample preparation kit were ligated using LigFast (Promega) and DNAs were amplified by PCR using primers provided in the IlluminaTruSeq DNA sample preparation kit and Phusion DNA polymerase (NEB).  Products of the ligation reaction and PCR amplification in the range 300-400 bp were purified by 2% agarose gel electrophoresis.  DNA concentrations were measured using Qubit™ dsDNA HS Assay Kits (Invitrogen). PGCGROWTHCONDITIONS
Escherichia coli CFT073 PGCGROWTHCONDITIONS
Genome_build: CFT073(AE014075.1) PGCGROWTHCONDITIONS
NsrR_ChIPSeq_rep1 PGCGROWTHCONDITIONS
NsrR_ChIPSeq_rep2 PGCGROWTHCONDITIONS
NsrR_ChIPSeq_rep3 PGCGROWTHCONDITIONS
NsrR_input PGCGROWTHCONDITIONS
peaks were called using MACS2 with default parameters PGCGROWTHCONDITIONS
samples were grown aerobically in rich media PGCGROWTHCONDITIONS
strain: CFT073 nsrR::3X-Flag tag PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: bed format peak file generated from MACS2 PGCGROWTHCONDITIONS
uropathogenic Escherichia coli (UPEC) PGCGROWTHCONDITIONS
Escherichia coli CFT073 PGCGROWTHCONDITIONS
Genome_build: CFT073(AE014075.1) PGCGROWTHCONDITIONS
genotype: deltahmp deltanrfA deltanorVW PGCGROWTHCONDITIONS
(-NO)1 PGCGROWTHCONDITIONS
(+NO)1 PGCGROWTHCONDITIONS
(-NO)2 PGCGROWTHCONDITIONS
(+NO)2 PGCGROWTHCONDITIONS
(-NO)3 PGCGROWTHCONDITIONS
(+NO)3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the CFT073 genome using bowtie (version 0.12.8) PGCGROWTHCONDITIONS
Samples were grown anaerobically in MOPS minimal media supplemented with casamino acids using glucose as the carbon source. 20mM nitrate was added to (+NO) cultures for inducing nitrosative stress. PGCGROWTHCONDITIONS
strain: CFT073 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; column1: transcript id; column2: TPM value PGCGROWTHCONDITIONS
Total Rna was extracted from cultures using Qiagen RNeasy Protect Bacteria Mini Kit. For rRNA depletion, samples were treated with the MICROBExpressTM Bacterial mRNA Enrichment Kit (Life Technologies) according to the manufacturer’s instructions.  Samples were cleaned with the Zymo RNA Clean and ConcentratorTM (Zymo Research) and then subjected to a second cycle of rRNA depletion.  RNA was recovered by ethanol precipitation. PGCGROWTHCONDITIONS
TPM (transcripts per million) was calculated by RSEM(version 1.2.19) PGCGROWTHCONDITIONS
uropathogenic Escherichia coli (UPEC) grown with nitrosative stress PGCGROWTHCONDITIONS
uropathogenic Escherichia coli (UPEC) grown without nitrosative stress PGCGROWTHCONDITIONS
DnaK deletant_37C PGCGROWTHCONDITIONS
E.coli gene expression data in deletion of chaperone DnaK PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
strain background: BW25113 PGCGROWTHCONDITIONS
The signal PGCGROWTHCONDITIONS
Total RNA was isolated from strains using NucleoSpin RNAII kit (Macherey-Nagel Corporation) following the instruction. RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray. PGCGROWTHCONDITIONS
WT_37C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 10 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 2 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 4 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 6 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 8 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 before paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 with a precise deletion in soxR and 10 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 with a precise deletion in soxR and 2 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 with a precise deletion in soxR and 4 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 with a precise deletion in soxR and 6 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 with a precise deletion in soxR and 8 minutes paraquat treatment PGCGROWTHCONDITIONS
Escherichia coli MG1655 with a precise deletion in soxR before paraquat treatment PGCGROWTHCONDITIONS
M1655 wild type at t0, rep1 PGCGROWTHCONDITIONS
M1655 wild type at t0, rep2 PGCGROWTHCONDITIONS
M1655 wild type at t10, rep1 PGCGROWTHCONDITIONS
M1655 wild type at t10, rep2 PGCGROWTHCONDITIONS
M1655 wild type at t2, rep1 PGCGROWTHCONDITIONS
M1655 wild type at t2, rep2 PGCGROWTHCONDITIONS
M1655 wild type at t4, rep1 PGCGROWTHCONDITIONS
M1655 wild type at t4, rep2 PGCGROWTHCONDITIONS
M1655 wild type at t6, rep1 PGCGROWTHCONDITIONS
M1655 wild type at t6, rep2 PGCGROWTHCONDITIONS
M1655 wild type at t8, rep1 PGCGROWTHCONDITIONS
M1655 wild type at t8, rep2 PGCGROWTHCONDITIONS
M1655 with deletion in soxR at t0, rep1 PGCGROWTHCONDITIONS
M1655 with deletion in soxR at t10, rep1 PGCGROWTHCONDITIONS
M1655 with deletion in soxR at t2, rep1 PGCGROWTHCONDITIONS
M1655 with deletion in soxR at t4, rep1 PGCGROWTHCONDITIONS
M1655 with deletion in soxR at t6, rep1 PGCGROWTHCONDITIONS
M1655 with deletion in soxR at t8, rep1 PGCGROWTHCONDITIONS
Overnight cultures were inoculated 1:100 into 20ml of EZ Rich Defined Medium (Neidhardt et al., 1974) in 125 ml Erlenmeyer flasks and grown at 37oC and 250 rpm in a reciprocating water bath. PGCGROWTHCONDITIONS
Paraquat was added to growing cultures at a final concentration of 250 ?M. Samples (1.4ml) were taken every 2 minutes following paraquat treatment for the length of the time course, and flash-frozen by immersion of the tubes in liquid nitrogen.  The cells were collected by centrifugation for 1 minute at 13,000 rpm, PGCGROWTHCONDITIONS
The data were analyzed using Robust Multi-Array average as implemented in Bioconductor PGCGROWTHCONDITIONS
Total RNA was isolated using Qiagen RNeasy Mini Kit and treated with DNase I PGCGROWTHCONDITIONS
agitation speed: 1200 rpm PGCGROWTHCONDITIONS
agitation speed: 600 rpm PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Data filtering was done with in-house script with the set value as follows: Removal if % of N nucleotide is more than 10%, if more than 40% of the nucleotide is Q20 or less, if average quality of the reads is less than Q20. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Expression of introduced enzymes for 3-HP productionm was induced by 0.05mM IPTG and 50 µM vitamin B12 when the cell reached at the early-exponential growth phase. T PGCGROWTHCONDITIONS
fermentation time: 20h PGCGROWTHCONDITIONS
fermentation time: 30h PGCGROWTHCONDITIONS
fermentation time: 40h PGCGROWTHCONDITIONS
Genome_build: http: PGCGROWTHCONDITIONS
Illumina Casava 1.8.2 software used for basecalling with default parameter. PGCGROWTHCONDITIONS
Read alignment was performed with BWA (version 0.6.2) with default parameter. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity sequence, then mapped to E.coli W3110 whole genome. PGCGROWTHCONDITIONS
SH0003 30h PGCGROWTHCONDITIONS
SH0012 20h PGCGROWTHCONDITIONS
SH0012 30h PGCGROWTHCONDITIONS
Sh0012 40h PGCGROWTHCONDITIONS
SH0012 and SH0003 were fermented in a 5.0L jar-fermenter with a 2.0 working voulume of modified R medium (20g PGCGROWTHCONDITIONS
SH0012 no rpm change PGCGROWTHCONDITIONS
SH0012 no vitamin B12 PGCGROWTHCONDITIONS
strain: SH0003 PGCGROWTHCONDITIONS
strain: SH0012 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel files include FPKM values for each sample. PGCGROWTHCONDITIONS
The bacterial cells from 5L fermentation were collected at 20h, 30h, 40h and centrifuged for 5min to pellet the cells. The cells then mixed with 500mL of RNA protectant bacterial reagents to stabilize RNA and stored at -80°C until use. Total RNAs were isolated using RNeasy mini kit and were treated with DNase to remove DNA. PGCGROWTHCONDITIONS
The RNA-Seq library was constructed with TruSeq RNA Preparation Kit. PGCGROWTHCONDITIONS
Transcript assembly an quantification was performed using a protocols from Trapnell et al., and Li et al. Fragments Per Kilobases of exon per million (FPKM) were calculated. PGCGROWTHCONDITIONS
Cells grown aerobically to exponential phase (OD600 = 0.8) in LB media at 37C were harvested. PGCGROWTHCONDITIONS
E. coli expressing dr1558 replicate 1 PGCGROWTHCONDITIONS
E. coli expressing dr1558 replicate 2 PGCGROWTHCONDITIONS
E. coli expressing dr1558 replicate 3 PGCGROWTHCONDITIONS
E. coli harboring pRadGro replicate 1 PGCGROWTHCONDITIONS
E. coli harboring pRadGro replicate 2 PGCGROWTHCONDITIONS
E. coli harboring pRadGro replicate 3 PGCGROWTHCONDITIONS
Ec-pR VS Ec-1558 rep1 PGCGROWTHCONDITIONS
Ec-pR VS Ec-1558 rep2 PGCGROWTHCONDITIONS
Ec-pR VS Ec-1558 rep3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Non-treatment PGCGROWTHCONDITIONS
strain information: E. coli harboring empty vector (pRADgro), used as a control strain PGCGROWTHCONDITIONS
strain information: E. coli harboring pRADgro::dr1558 PGCGROWTHCONDITIONS
The genes were considered differentially expressed when the logarithmic gene expression ratios had a 2-fold difference in the expression level. The significance of the data was determined using Student’s t test. P-values of less than 0.01 were considered significant. PGCGROWTHCONDITIONS
The genes were filtered by removing the flag-out genes in each experiment. The gene expression was normalized through LOWESS regression for 3 datasets obtained from 3 biological replicates. PGCGROWTHCONDITIONS
Total RNA extracted using RiboEX reagent (GeneAll, Korea), treated with Dnase, and purified using the Rneasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions. PGCGROWTHCONDITIONS
0' in minimal medium +0.2% glu, 25 ug total RNA PGCGROWTHCONDITIONS
0' in min med +0.2% glu, 25ug total RNA PGCGROWTHCONDITIONS
0' minimal + 0.2% glu, 25 ug total RNA PGCGROWTHCONDITIONS
0' minimal +02% glu, 25 ug total RNA PGCGROWTHCONDITIONS
0' minimal medium + 0.2% glu, 25 ug total PGCGROWTHCONDITIONS
Adaptor Sequences were removed using fastx_clipper. (http: PGCGROWTHCONDITIONS
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit. PGCGROWTHCONDITIONS
bacterial cell lysates_input PGCGROWTHCONDITIONS
bacterial cell lysates_RecA-ChIP-seq PGCGROWTHCONDITIONS
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1 PGCGROWTHCONDITIONS
Cells were grown in M9 minimal media supplemented with 0.2% casamino acids, 0.5% glucose 5μM CaCl2 and 1mM MgSO4 at 37°C to and OD600nm of 0.2-0.25 PGCGROWTHCONDITIONS
chip antibody: anti-RecA antibody PGCGROWTHCONDITIONS
chip antibody cat.#: ab63797 PGCGROWTHCONDITIONS
chip antibody vendor: Abcam PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Data collapsed using fastx collapser to remove identical sequencing reads (http: PGCGROWTHCONDITIONS
DL4899 PGCGROWTHCONDITIONS
DL4900 PGCGROWTHCONDITIONS
DL4900_input PGCGROWTHCONDITIONS
DL5215 PGCGROWTHCONDITIONS
DL5322 PGCGROWTHCONDITIONS
DL5324 PGCGROWTHCONDITIONS
DL5326 PGCGROWTHCONDITIONS
DL5328 PGCGROWTHCONDITIONS
DL5330 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 MG1655 NC000913.3 PGCGROWTHCONDITIONS
Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M PGCGROWTHCONDITIONS
reads were mapped to the E. coli K12 MG1655 (NC000913.3) genome using Novoalign version 2.07  (www.novocraft.com) - Example: (novoalign -f DL4900_clip_clp.fasta -d NC000913.3.nix -r Random > DL4900.novo) PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- cynX::GmR lacZY::χχχ  mhpA::χχχ rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχ  mhpA::χχχ rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχχ mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχχχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+ PGCGROWTHCONDITIONS
strain details: lacIq lacZχ- lacZ::246pal cynX::GmR lacZY::χχχχχχ  mhpA::χχχ codBχ- prpEχ- mhpCχ- cynXχ- rph+ PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt files including count data for the whole genome PGCGROWTHCONDITIONS
yPileup was used to generate count data for the whole genome - Example:  pyPileup.py --file_type=novo -f DL4900.novo --tab=NC000913.3.tab --chr=Wholechom.txt.gz -- ignorestrand PGCGROWTHCONDITIONS
15' 10 ug PGCGROWTHCONDITIONS
15' 15 ug PGCGROWTHCONDITIONS
15'+50ug PGCGROWTHCONDITIONS
Aeration was initiated at 1 l PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
batch culture rep1, 0.5 min PGCGROWTHCONDITIONS
batch culture rep1, 0 min PGCGROWTHCONDITIONS
batch culture rep1, 10 min PGCGROWTHCONDITIONS
batch culture rep1, 1 min PGCGROWTHCONDITIONS
batch culture rep1, 2 min PGCGROWTHCONDITIONS
batch culture rep1, 5 min PGCGROWTHCONDITIONS
batch culture rep2, 0.5 min PGCGROWTHCONDITIONS
batch culture rep2, 0 min PGCGROWTHCONDITIONS
batch culture rep2, 10 min PGCGROWTHCONDITIONS
batch culture rep2, 1 min PGCGROWTHCONDITIONS
batch culture rep2, 2 min PGCGROWTHCONDITIONS
batch culture rep2, 5 min PGCGROWTHCONDITIONS
batch culture rep3, 0.5 min PGCGROWTHCONDITIONS
batch culture rep3, 0 min PGCGROWTHCONDITIONS
batch culture rep3, 10 min PGCGROWTHCONDITIONS
batch culture rep3, 1 min PGCGROWTHCONDITIONS
batch culture rep3, 2 min PGCGROWTHCONDITIONS
batch culture rep3, 5 min PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0.5 min PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
time: 1 min PGCGROWTHCONDITIONS
time: 2 min PGCGROWTHCONDITIONS
time: 5 min PGCGROWTHCONDITIONS
15' in minimal medium +0.2% glu, 25 ug total RNA PGCGROWTHCONDITIONS
15' in min med +0.2% glu+50ug PGCGROWTHCONDITIONS
15' vs 0' in minimal medium +0.2% glu PGCGROWTHCONDITIONS
agent: control PGCGROWTHCONDITIONS
agent: CORM-401 PGCGROWTHCONDITIONS
Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Continuous aerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401 PGCGROWTHCONDITIONS
Continuous anaerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401 PGCGROWTHCONDITIONS
culture conditions: aerobic PGCGROWTHCONDITIONS
culture conditions: anaerobic PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 10 Cy5 0 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 20 Cy5 0 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 40 Cy5 0 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 80 Cy5 0 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 10 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 20 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 2.5 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 40 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 5 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 80 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 2.5 Cy5 0 PGCGROWTHCONDITIONS
Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 5 Cy5 0 PGCGROWTHCONDITIONS
strain: Wild type strain MG1655 PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
time: 20 min PGCGROWTHCONDITIONS
time: 2.5 min PGCGROWTHCONDITIONS
time: 40 min PGCGROWTHCONDITIONS
time: 5 min PGCGROWTHCONDITIONS
time: 80 min PGCGROWTHCONDITIONS
Total RNA extracted using Trizol following manufacturer's instructions PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
K12 WT 3110 PGCGROWTHCONDITIONS
MasterPure RNA purification Kit PGCGROWTHCONDITIONS
Overnight culture PGCGROWTHCONDITIONS
phoU_1 PGCGROWTHCONDITIONS
phoU_2 PGCGROWTHCONDITIONS
phoU_3 PGCGROWTHCONDITIONS
phoU gene mutant PGCGROWTHCONDITIONS
phoU gene mutant; minimal medium PGCGROWTHCONDITIONS
The data were analyzed with GCOS 1.4 software.  All probe sets scaling was performed with a target signal value of 500.  No normalization was performed. PGCGROWTHCONDITIONS
wildtype strain; minimal medium PGCGROWTHCONDITIONS
WT3110_1 PGCGROWTHCONDITIONS
WT3110_2 PGCGROWTHCONDITIONS
WT3110_3 PGCGROWTHCONDITIONS
30' 10 ug PGCGROWTHCONDITIONS
30' 15 ug PGCGROWTHCONDITIONS
30'+50ug PGCGROWTHCONDITIONS
30' in minimal medium +0.2% glu, 25 ug total RNA PGCGROWTHCONDITIONS
30' in min med +0.2% glu+50ug PGCGROWTHCONDITIONS
30' vs 0' in minimal medium +0.2% glu PGCGROWTHCONDITIONS
BL21(DE3) HPA 0mM PGCGROWTHCONDITIONS
BL21(DE3) HPA 3mM PGCGROWTHCONDITIONS
BL21(DE3) with 3 mM of heptanoic acid PGCGROWTHCONDITIONS
BL21(DE3) without heptanoic acid PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
K12 MG1655 with 10 mM of heptanoic acid PGCGROWTHCONDITIONS
K12 MG1655 without heptanoic acid PGCGROWTHCONDITIONS
metabolic response: BL21(DE3) is very susceptible to heptanoic acid, because several acid resistance systems stay inactive under this stress condition PGCGROWTHCONDITIONS
metabolic response: K12 MG1655 activates various acid resistance systems under heptanoic acid stress PGCGROWTHCONDITIONS
MG1655 HPA 0mM PGCGROWTHCONDITIONS
MG1655 HPA 10mM PGCGROWTHCONDITIONS
strain: BL21(DE3) PGCGROWTHCONDITIONS
strain: K12 MG1655 PGCGROWTHCONDITIONS
stress: control PGCGROWTHCONDITIONS
stress: heptanoic acid PGCGROWTHCONDITIONS
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3.1 (Agilent Technology, USA).  Normalization for Agilent one-color method was performed, which is Data transformation : Set measurements less than 5.0 to 5.0 and Per Chip :Normalize to 50th percentage. PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol (Invitrogen) PGCGROWTHCONDITIONS
When E. coli cells were cultivated to the exponential growth phase (OD600 = 0.5) in Riesenberg medium, 3 or 10 mM heptanoic acid was treated to BL21(DE3) and K-12 MG1655, respectively. After 3 h incubation, the E. coli cells were harvested for transcriptome analysis PGCGROWTHCONDITIONS
aspC KO rep1 PGCGROWTHCONDITIONS
aspC KO rep2 PGCGROWTHCONDITIONS
aspC KO rep3 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysA KO rep1 PGCGROWTHCONDITIONS
cysA KO rep2 PGCGROWTHCONDITIONS
cysA KO rep3 PGCGROWTHCONDITIONS
cysG KO LB rep1 PGCGROWTHCONDITIONS
cysG KO LB rep2 PGCGROWTHCONDITIONS
cysH KO LB rep1 PGCGROWTHCONDITIONS
cysH KO LB rep2 PGCGROWTHCONDITIONS
dcd KO LB rep1 PGCGROWTHCONDITIONS
dcd KO LB rep2 PGCGROWTHCONDITIONS
dcd KO M9 rep1 PGCGROWTHCONDITIONS
dcd KO M9 rep2 PGCGROWTHCONDITIONS
entF KO rep1 PGCGROWTHCONDITIONS
entF KO rep2 PGCGROWTHCONDITIONS
entF KO rep3 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fadr KO LB rep1 PGCGROWTHCONDITIONS
fadr KO LB rep2 PGCGROWTHCONDITIONS
fadr KO M9 rep1 PGCGROWTHCONDITIONS
fadr KO M9 rep2 PGCGROWTHCONDITIONS
fepA KO LB rep1 PGCGROWTHCONDITIONS
fepA KO LB rep2 PGCGROWTHCONDITIONS
fepA KO M9 rep1 PGCGROWTHCONDITIONS
fepA KO M9 rep2 PGCGROWTHCONDITIONS
fliY KO rep1 PGCGROWTHCONDITIONS
fliY KO rep2 PGCGROWTHCONDITIONS
fliY KO rep3 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB PGCGROWTHCONDITIONS
gabT KO rep1 PGCGROWTHCONDITIONS
gabT KO rep2 PGCGROWTHCONDITIONS
gabT KO rep3 PGCGROWTHCONDITIONS
galE KO rep1 PGCGROWTHCONDITIONS
galE KO rep2 PGCGROWTHCONDITIONS
galE KO rep3 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
kefB KO rep1 PGCGROWTHCONDITIONS
kefB KO rep2 PGCGROWTHCONDITIONS
kefB KO rep3 PGCGROWTHCONDITIONS
khc KO rep1 PGCGROWTHCONDITIONS
khc KO rep2 PGCGROWTHCONDITIONS
khc KO rep3 PGCGROWTHCONDITIONS
lacA KO LB rep1 PGCGROWTHCONDITIONS
lacA KO LB rep2 PGCGROWTHCONDITIONS
lacA KO M9 rep1 PGCGROWTHCONDITIONS
lacA KO M9 rep2 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
lplA KO rep1 PGCGROWTHCONDITIONS
lplA KO rep2 PGCGROWTHCONDITIONS
lplA KO rep3 PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mgtA KO rep1 PGCGROWTHCONDITIONS
mgtA KO rep2 PGCGROWTHCONDITIONS
mgtA KO rep3 PGCGROWTHCONDITIONS
mhpD KO rep1 PGCGROWTHCONDITIONS
mhpD KO rep2 PGCGROWTHCONDITIONS
mhpD KO rep3 PGCGROWTHCONDITIONS
Parent LB rep1 PGCGROWTHCONDITIONS
Parent LB rep2 PGCGROWTHCONDITIONS
Parent M9 rep1 PGCGROWTHCONDITIONS
Parent M9 rep2 PGCGROWTHCONDITIONS
ppk KO LB rep1 PGCGROWTHCONDITIONS
ppk KO LB rep2 PGCGROWTHCONDITIONS
ppk KO M9 rep1 PGCGROWTHCONDITIONS
ppk KO M9 rep2 PGCGROWTHCONDITIONS
putP KO rep1 PGCGROWTHCONDITIONS
putP KO rep2 PGCGROWTHCONDITIONS
putP KO rep3 PGCGROWTHCONDITIONS
rfbA KO rep1 PGCGROWTHCONDITIONS
rfbA KO rep2 PGCGROWTHCONDITIONS
rfbA KO rep3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sdhC KO rep1 PGCGROWTHCONDITIONS
sdhC KO rep2 PGCGROWTHCONDITIONS
sdhC KO rep3 PGCGROWTHCONDITIONS
strain PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
trpD KO rep1 PGCGROWTHCONDITIONS
trpD KO rep2 PGCGROWTHCONDITIONS
trpD KO rep3 PGCGROWTHCONDITIONS
ugpC KO rep1 PGCGROWTHCONDITIONS
ugpC KO rep2 PGCGROWTHCONDITIONS
ugpC KO rep3 PGCGROWTHCONDITIONS
Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, cysG KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, cysH KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, dcd KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, dcd KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, fadR KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, fadR KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, fepA KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, fepA KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, galE KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, lacA KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, lacA KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, ppk KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, ppk KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, WT, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Whole cell, wzc KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, wzc KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, yghD KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Whole cell, yghD KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
WT rep1 PGCGROWTHCONDITIONS
WT rep2 PGCGROWTHCONDITIONS
WT rep3 PGCGROWTHCONDITIONS
wzc KO LB rep1 PGCGROWTHCONDITIONS
wzc KO LB rep2 PGCGROWTHCONDITIONS
wzc KO M9 rep1 PGCGROWTHCONDITIONS
wzc KO M9 rep2 PGCGROWTHCONDITIONS
yghD KO LB rep1 PGCGROWTHCONDITIONS
yghD KO LB rep2 PGCGROWTHCONDITIONS
yghD KO M9 rep1 PGCGROWTHCONDITIONS
yghD KO M9 rep2 PGCGROWTHCONDITIONS
5-azacytidine-treated PGCGROWTHCONDITIONS
Agilent Feature Extract software performed background normalization and LOWESS correction for dye bias. Non-E. coli K-12 probes were removed from the dataset, as the BW25113 strain is a K-12 strain. PGCGROWTHCONDITIONS
Cells were grown in the absence and presence of 0.005 mg PGCGROWTHCONDITIONS
early stationary phase 1 PGCGROWTHCONDITIONS
early stationary phase 2 PGCGROWTHCONDITIONS
early stationary phase 3 PGCGROWTHCONDITIONS
early stationary phase 4 PGCGROWTHCONDITIONS
early stationary phase 5 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli cells were grown in LB at 37oC with shaking at 250 RPM PGCGROWTHCONDITIONS
log phase 1 PGCGROWTHCONDITIONS
log phase 2 PGCGROWTHCONDITIONS
log phase 3 PGCGROWTHCONDITIONS
log phase 4 PGCGROWTHCONDITIONS
log phase 5 PGCGROWTHCONDITIONS
phase: early stationary phase PGCGROWTHCONDITIONS
phase: log phase PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Total RNA was isolated with the MasterPure RNA Isolation Kit (Epicentre), enriched for mRNA using the mRNA Prokaryotic mRNA Isolation Kit (Epicentre), and polyadenylated with kit all based on the manufacturer's instructions PGCGROWTHCONDITIONS
untreated PGCGROWTHCONDITIONS
150 minutes growth  in LB PGCGROWTHCONDITIONS
240 minutes growth  in LB PGCGROWTHCONDITIONS
360 minutes growth  in LB PGCGROWTHCONDITIONS
90 minutes growth  in LB PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 150 minutes PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 240 minutes PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 360 minutes PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 90 minutes PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 fis::kan grown 150 minutes PGCGROWTHCONDITIONS
Escherichia coli MG1655 fis::kan grown 240 minutes PGCGROWTHCONDITIONS
Escherichia coli MG1655 fis::kan grown 360 minutes PGCGROWTHCONDITIONS
Escherichia coli MG1655 fis::kan grown 90 minutes PGCGROWTHCONDITIONS
fis 150 minutes growth rep1 PGCGROWTHCONDITIONS
fis 150 minutes growth rep2 PGCGROWTHCONDITIONS
fis 150 minutes growth rep3 PGCGROWTHCONDITIONS
fis 240 minutes growth rep1 PGCGROWTHCONDITIONS
fis 240 minutes growth rep2 PGCGROWTHCONDITIONS
fis 240 minutes growth rep3 PGCGROWTHCONDITIONS
fis 360 minutes growth rep1 PGCGROWTHCONDITIONS
fis 360 minutes growth rep2 PGCGROWTHCONDITIONS
fis 360 minutes growth rep3 PGCGROWTHCONDITIONS
fis 90 minutes growth rep1 PGCGROWTHCONDITIONS
fis 90 minutes growth rep2 PGCGROWTHCONDITIONS
fis 90 minutes growth rep3 PGCGROWTHCONDITIONS
fis  Escherichia coli PGCGROWTHCONDITIONS
MasterPure RNA purification Kit per manufacturers protocol PGCGROWTHCONDITIONS
Saturated E. coli cultures were diluted in LB toan OD.of  0.05 OD600, grown at 37 degrees Celsius PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.  Data from this sample were collected using Affy Ecoli anti-sense chip (2001; platform ID GPL4940), but because the analysis software failed to recognize the correct platform, we reformatted the data to match the newer (and mostly equivalent) platform GPL199 (Affy Ecoli anti-sense chip version 2, 2002).  Because, however, not all of the probes on the new platform were present on the old platform, data for some probes were unavailable and labeled in the 'remapped' dataset as 'NULL' to indicate they were missing.  While the following data are therefore formatted using ID_REFs that match GPL199, the CEL file contains the raw data (not 'remapped') and thus corresponds to the actual array used (GPL4940, Ecoli antisense chip, 2001). PGCGROWTHCONDITIONS
150 minutes growth  in LB PGCGROWTHCONDITIONS
240 minutes growth  in LB PGCGROWTHCONDITIONS
360 minutes growth  in LB PGCGROWTHCONDITIONS
90 minutes growth  in LB PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 150 minutes PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 240 minutes PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 360 minutes PGCGROWTHCONDITIONS
Cells were grown in LB at 37 degrees celsius with shaking for 90 minutes PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli MG1655 wt grown 150 minutes PGCGROWTHCONDITIONS
Escherichia coli MG1655 wt grown 240 minutes PGCGROWTHCONDITIONS
Escherichia coli MG1655 wt grown 360 minutes PGCGROWTHCONDITIONS
Escherichia coli MG1655 wt grown 90 minutes PGCGROWTHCONDITIONS
MasterPure RNA purification Kit per manufacturers protocol PGCGROWTHCONDITIONS
Saturated E. coli cultures were diluted in LB to an OD.of  0.05 OD600, grown at 37 degrees Celsius PGCGROWTHCONDITIONS
Saturated E. coli cultures were diluted in LB toan OD.of  0.05 OD600, grown at 37 degrees Celsius PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.  Data from this sample were collected using Affy Ecoli anti-sense chip (2001; platform ID GPL4940), but because the analysis software failed to recognize the correct platform, we reformatted the data to match the newer (and mostly equivalent) platform GPL199 (Affy Ecoli anti-sense chip version 2, 2002).  Because, however, not all of the probes on the new platform were present on the old platform, data for some probes were unavailable and labeled in the 'remapped' dataset as 'NULL' to indicate they were missing.  While the following data are therefore formatted using ID_REFs that match GPL199, the CEL file contains the raw data (not 'remapped') and thus corresponds to the actual array used (GPL4940, Ecoli antisense chip, 2001). PGCGROWTHCONDITIONS
wildtype Escherichia coli PGCGROWTHCONDITIONS
wt 150 minutes growth rep1 PGCGROWTHCONDITIONS
wt 150 minutes growth rep2 PGCGROWTHCONDITIONS
wt 150 minutes growth rep3 PGCGROWTHCONDITIONS
wt 240 minutes growth rep1 PGCGROWTHCONDITIONS
wt 240 minutes growth rep2 PGCGROWTHCONDITIONS
wt 240 minutes growth rep3 PGCGROWTHCONDITIONS
wt 360 minutes growth rep1 PGCGROWTHCONDITIONS
wt 360 minutes growth rep2 PGCGROWTHCONDITIONS
wt 360 minutes growth rep3 PGCGROWTHCONDITIONS
wt 90 minutes growth rep1 PGCGROWTHCONDITIONS
wt 90 minutes growth rep2 PGCGROWTHCONDITIONS
wt 90 minutes growth rep3 PGCGROWTHCONDITIONS
All raw FastQ files generated were filtered using FASTX-Toolkit (http: PGCGROWTHCONDITIONS
Enterohemorrhagic Escherichia coli O157:H7 strain EDL933 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655.2 PGCGROWTHCONDITIONS
genotype: {delta}hns PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
hns_1 PGCGROWTHCONDITIONS
hns_2 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS
phase: logarithmic phase PGCGROWTHCONDITIONS
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628) PGCGROWTHCONDITIONS
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM PGCGROWTHCONDITIONS
The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS. PGCGROWTHCONDITIONS
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138) PGCGROWTHCONDITIONS
wt_1 PGCGROWTHCONDITIONS
wt_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_EE_1 PGCGROWTHCONDITIONS
rpoS_EE_2 PGCGROWTHCONDITIONS
rpoS_LS_1 PGCGROWTHCONDITIONS
rpoS_LS_2 PGCGROWTHCONDITIONS
rpoS_ME_1 PGCGROWTHCONDITIONS
rpoS_ME_2 PGCGROWTHCONDITIONS
rpoS_S_1 PGCGROWTHCONDITIONS
rpoS_S_2 PGCGROWTHCONDITIONS
rpoS_TS_1 PGCGROWTHCONDITIONS
rpoS_TS_2 PGCGROWTHCONDITIONS
rsd_EE_1 PGCGROWTHCONDITIONS
rsd_EE_2 PGCGROWTHCONDITIONS
rsd_LS_1 PGCGROWTHCONDITIONS
rsd_LS_2 PGCGROWTHCONDITIONS
rsd_ME_1 PGCGROWTHCONDITIONS
rsd_ME_2 PGCGROWTHCONDITIONS
rsd_S_1 PGCGROWTHCONDITIONS
rsd_S_2 PGCGROWTHCONDITIONS
rsdssrS_EE_1 PGCGROWTHCONDITIONS
rsdssrS_EE_2 PGCGROWTHCONDITIONS
rsdssrS_LS_1 PGCGROWTHCONDITIONS
rsdssrS_LS_2 PGCGROWTHCONDITIONS
rsdssrS_ME_1 PGCGROWTHCONDITIONS
rsdssrS_ME_2 PGCGROWTHCONDITIONS
rsdssrS_S_1 PGCGROWTHCONDITIONS
rsdssrS_S_2 PGCGROWTHCONDITIONS
rsdssrS_TS_1 PGCGROWTHCONDITIONS
rsdssrS_TS_2 PGCGROWTHCONDITIONS
rsd_TS_1 PGCGROWTHCONDITIONS
rsd_TS_2 PGCGROWTHCONDITIONS
ssrS_EE_1 PGCGROWTHCONDITIONS
ssrS_EE_2 PGCGROWTHCONDITIONS
ssrS_LS_1 PGCGROWTHCONDITIONS
ssrS_LS_2 PGCGROWTHCONDITIONS
ssrS_ME_1 PGCGROWTHCONDITIONS
ssrS_ME_2 PGCGROWTHCONDITIONS
ssrS_S_1 PGCGROWTHCONDITIONS
ssrS_S_2 PGCGROWTHCONDITIONS
ssrS_TS_1 PGCGROWTHCONDITIONS
ssrS_TS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_EE_1 PGCGROWTHCONDITIONS
wt_EE_2 PGCGROWTHCONDITIONS
wt_LS_1 PGCGROWTHCONDITIONS
wt_LS_2 PGCGROWTHCONDITIONS
wt_ME_1 PGCGROWTHCONDITIONS
wt_ME_2 PGCGROWTHCONDITIONS
wt_S_1 PGCGROWTHCONDITIONS
wt_S_2 PGCGROWTHCONDITIONS
wt_TS_1 PGCGROWTHCONDITIONS
wt_TS_2 PGCGROWTHCONDITIONS
chip antibody manufacturer PGCGROWTHCONDITIONS
chip antibody: Monoclonal anti-FLAG antibody, Murine  IgG PGCGROWTHCONDITIONS
ChIP-exo reads were aligned using BWA with  default parameters PGCGROWTHCONDITIONS
E. coli and S. Typhimurium cells (at mid-exponential growth phase) were fixed with formaldehyde (1% final concentration) for  20 min at 30°C with shaking. The crosslinking reaction was then quenched by the addition of glycine (0.33M final concentrationg) for 5 minutes at room temperature with gentle mixing.  Cells where then lysed on ice with lysozyme and sonication. PGCGROWTHCONDITIONS
E. coli cells were grown in Kornberg medium (1.1% [wt PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
Genome_build: NC_016856.1 PGCGROWTHCONDITIONS
Library strategy: ChIP-exo PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
Peaks on opposing strands were paired with Genetrack (u=0, d=80, b=2, m=mode) PGCGROWTHCONDITIONS
Peaks were called with GeneTrack 1.0.3 (s=5, e=10) PGCGROWTHCONDITIONS
Peconic LLC performed data processing PGCGROWTHCONDITIONS
Samples were used for on-bead enzymatic reactions of the ChIP-exo procedure and Illumina Tru-seq sequencing libraries were construction as described in Rhee and Pugh, 2012 PGCGROWTHCONDITIONS
Singleton peaks (standard deviation =0) and peaks without matched peaks on the opposing strand where discarded PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
S. Typhimurium cells were grown in LB (supplemented with 10mM glucose) to mid-exponential phase (OD600 = ~0.6) at 37C and shaking 250rpm PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Bedgraphs files representing the extracted peak data PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: chromosome chromosomeStartPosition chromosomeStopPosition readCoverage(positive values on + strand, negative on - strand) PGCGROWTHCONDITIONS
UvrY - ChIP-exo PGCGROWTHCONDITIONS
UvrY (Response regulator of the BarA PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Cells were grown at 37°C, 200 rpm in M9 glucose, for 16 hours (stationary phase). PGCGROWTHCONDITIONS
chip antibody: None PGCGROWTHCONDITIONS
chip antibody: RpoS (Neoclone cat. no. WP009) PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Cross-linked cells were harvested by centrifugation, washed thrice with ice-cold TBS (pH 7.5), resuspended in 1 ml lysis buffer [10 mM Tris (pH 8.0), 20% sucrose, 50 mM NaCl, 10 mM EDTA, 20 mg PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Files were coverted to .bam format using samtools PGCGROWTHCONDITIONS
Formaldehyde was added to a final concentration of 1%. After incubation for 20 minutes, glycine was added to a final concentration of 0.5 M and incubated for 5 minutes. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: MG1655 del ssrS PGCGROWTHCONDITIONS
genotype: MG1655 wild-type PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected. Files were coverted to .bam format using samtools. The MACS 2.1.0 software was used to call peaks. Peaks overlapping in both replicates were selected for further analysis. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected. Files were coverted to .bam format using samtools. The MACS 2.1.0 software was used to call peaks. Peaks overlapping in both replicates were selected for further analysis.  PGCGROWTHCONDITIONS
Reads were trimmed for quality using Trimmomatic-0.32 with a cutoff quality score of 20 PGCGROWTHCONDITIONS
ssrS_1_input PGCGROWTHCONDITIONS
ssrS_1_IP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .narrowPeak files output by macs2, giving peak start and end positions, as well as fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .narrowPeak files output by MACS, giving peak start and end positions, as well as fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start PGCGROWTHCONDITIONS
The MACS 2.1.0 software was used to call peaks. PGCGROWTHCONDITIONS
The MACS2 software was used to call peaks. PGCGROWTHCONDITIONS
wt_1_input PGCGROWTHCONDITIONS
wt_1_IP PGCGROWTHCONDITIONS
wt_2_input PGCGROWTHCONDITIONS
wt_2_IP PGCGROWTHCONDITIONS
Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of ~0.3-0.35) in MOPS minimal glucose media containing 10 µM FeSO4. PGCGROWTHCONDITIONS
Cells were treated with a stop solution of phenol and ethanol (Khodursky et al, Methods in Molecular Biology 2003), spun down, and flash frozen and stored at -80°C. PGCGROWTHCONDITIONS
culture condition: Aerobic cultures PGCGROWTHCONDITIONS
culture condition: Anaerobic cultures PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
∆fur Aerobic A PGCGROWTHCONDITIONS
∆fur Aerobic B PGCGROWTHCONDITIONS
∆fur Anaerobic A PGCGROWTHCONDITIONS
∆fur Anaerobic B PGCGROWTHCONDITIONS
Fur-minus_cDNA_Aerobic PGCGROWTHCONDITIONS
Fur-minus_cDNA_Anaerobic PGCGROWTHCONDITIONS
Fur-minus_RyhB-minus_cDNA_Aerobic PGCGROWTHCONDITIONS
Fur-minus_RyhB-minus_cDNA_Anaerobic PGCGROWTHCONDITIONS
∆fur ∆ryhB Aerobic A PGCGROWTHCONDITIONS
∆fur ∆ryhB Aerobic B PGCGROWTHCONDITIONS
∆fur ∆ryhB Anaerobic A PGCGROWTHCONDITIONS
∆fur ∆ryhB Anaerobic B PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Raw probe intensities were normalized across all samples using the Robust Multichip Average (RMA) algorithm in the NimbleScan software package (version 2.5). PGCGROWTHCONDITIONS
RMA normalized probe data was uploaded into the Mochiview visualization software where data cooresponding to the plus and minus strands were subtracted to get a strand-specific probe intesenity per base as reported in the processed data files. PGCGROWTHCONDITIONS
∆ryhB Aerobic PGCGROWTHCONDITIONS
∆ryhB Anaerobic PGCGROWTHCONDITIONS
RyhB-minus_cDNA_Aerobic_WIG.txt PGCGROWTHCONDITIONS
RyhB-minus_cDNA_Anaerobic_WIG.txt PGCGROWTHCONDITIONS
Total RNA was extracted using a hot phenol method (Khodursky et al, Methods in Molecular Biology 2003). PGCGROWTHCONDITIONS
Wild-type Aerobic A PGCGROWTHCONDITIONS
Wild-type Aerobic B PGCGROWTHCONDITIONS
Wild-type Anaerobic A PGCGROWTHCONDITIONS
Wild-type Anaerobic B PGCGROWTHCONDITIONS
Wild-type_cDNA_Aerobic PGCGROWTHCONDITIONS
Wild-type_cDNA_Anaerobic PGCGROWTHCONDITIONS
Cultures grown in MOPS minimal glucose media containing 10 µM FeSO4 PGCGROWTHCONDITIONS
Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
∆fur Anaerobic [IP vs nput] PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Input ∆fur Anaerobic PGCGROWTHCONDITIONS
ip antibody: affinity purified anti-Fur antibody PGCGROWTHCONDITIONS
IP ∆fur Anaerobic PGCGROWTHCONDITIONS
NimbleScan software package, version 2.5 (Roche NimbleGen) was used to extract the scanned data, which was subsequently qunatile normalized using the statistical program R. The sample data table contains the log2 ratio of the IP PGCGROWTHCONDITIONS
sample type: input control PGCGROWTHCONDITIONS
Sodium phosphate (1 PGCGROWTHCONDITIONS
Aerobic cultures PGCGROWTHCONDITIONS
Anaerobic cultures PGCGROWTHCONDITIONS
Anaerobic, Iron Deficient cultures PGCGROWTHCONDITIONS
Call peaks to and FDR 0.1, MOSAiCs PGCGROWTHCONDITIONS
Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng PGCGROWTHCONDITIONS
Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of ~0.3-0.35). PGCGROWTHCONDITIONS
chip antibody: Custom anti-Fur polyclonal antibody PGCGROWTHCONDITIONS
chip antibody: none PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Combined input PGCGROWTHCONDITIONS
Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur. PGCGROWTHCONDITIONS
Deconvolute peaks in close proximity, dPeak PGCGROWTHCONDITIONS
DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Aerobic A PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Aerobic B PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Aerobic C PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Anaerobic A PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Anaerobic B PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Anaerobic C PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Anaerobic, Iron Deficient A PGCGROWTHCONDITIONS
Fur IP ChIP-Seq Anaerobic, Iron Deficient B PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 K-12 genome version U00096.2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth medium: Combined input PGCGROWTHCONDITIONS
growth medium: MOPS minimal glucose media containing 10 µM FeSO4 PGCGROWTHCONDITIONS
growth medium: MOPS minimal glucose media containing 1 µM FeSO4 PGCGROWTHCONDITIONS
Input ChIP-Seq PGCGROWTHCONDITIONS
Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2 PGCGROWTHCONDITIONS
Reformat Illumina files to Sanger format, FASTQ Groomer PGCGROWTHCONDITIONS
Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection PGCGROWTHCONDITIONS
Scale data set to 20 million reads PGCGROWTHCONDITIONS
Sodium phosphate (1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment PGCGROWTHCONDITIONS
5' 10 ug PGCGROWTHCONDITIONS
5' 15 ug PGCGROWTHCONDITIONS
5'+50ug PGCGROWTHCONDITIONS
Bacteria were lyzed with lyzozyme and sonicated to shear DNA. TopoIV-DNA complexes were isolated with antibody . PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
chip antibody: antiFlag M2 PGCGROWTHCONDITIONS
chip antibody: none PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq reads were aligned to the E. coli NC_000913 genome using BWA 0.6.2 PGCGROWTHCONDITIONS
E. coli MG1655 parC::flag PGCGROWTHCONDITIONS
E. coli MG1655 parE::flag PGCGROWTHCONDITIONS
E. coli were grown in LB or minimal medium supplemented with casaminoacids (0,1%) and succinate (0,1%) until OD 0,2-0,4 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For ChIP-seq experiments E. coli culture were fixed with formaldehyde (1% final concentration); for NorfliP experiments TopoIV was crosslinked with Norfloxacin (2µM) PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
growth conditions: LB growth OD 0,3 PGCGROWTHCONDITIONS
growth conditions: LB growth OD 0,5 PGCGROWTHCONDITIONS
growth conditions: Minimal Medium A  supplemented with casaminoacids (0,1%) and succinate (0,2%),  OD 0,2 at 40°C PGCGROWTHCONDITIONS
Input ParC-flag 1 PGCGROWTHCONDITIONS
Input ParE-flag 1 PGCGROWTHCONDITIONS
Input ParE-flag 2 PGCGROWTHCONDITIONS
Input ParE-flag G1 PGCGROWTHCONDITIONS
Input ParE-flag G2 PGCGROWTHCONDITIONS
Input ParE-flag S20min PGCGROWTHCONDITIONS
Input ParE-flag S40min PGCGROWTHCONDITIONS
IP ParC-flag 1 PGCGROWTHCONDITIONS
IP ParE-flag 1 PGCGROWTHCONDITIONS
IP ParE-flag 2 PGCGROWTHCONDITIONS
IP ParE-flag G1 PGCGROWTHCONDITIONS
IP ParE-flag G2 PGCGROWTHCONDITIONS
IP ParE-flag S20min PGCGROWTHCONDITIONS
IP ParE-flag S40min PGCGROWTHCONDITIONS
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (FC-104-5001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. PGCGROWTHCONDITIONS
NorflIP Input ParC-flag 1 PGCGROWTHCONDITIONS
NorflIP Input ParC-flag 2 PGCGROWTHCONDITIONS
NorflIP Input ParE-flag 1 PGCGROWTHCONDITIONS
NorflIP IP ParC-flag 1 PGCGROWTHCONDITIONS
NorflIP IP ParC-flag 2 PGCGROWTHCONDITIONS
NorflIP IP ParE-flag 1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Enrichement (IP PGCGROWTHCONDITIONS
bla_0min PGCGROWTHCONDITIONS
bla_10min PGCGROWTHCONDITIONS
bla_15min PGCGROWTHCONDITIONS
bla_1min PGCGROWTHCONDITIONS
bla_2min PGCGROWTHCONDITIONS
bla_4min PGCGROWTHCONDITIONS
bla_6min PGCGROWTHCONDITIONS
bla_8min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
lacZ_0min PGCGROWTHCONDITIONS
lacZ_10min PGCGROWTHCONDITIONS
lacZ_15min PGCGROWTHCONDITIONS
lacZ_1min PGCGROWTHCONDITIONS
lacZ_2min PGCGROWTHCONDITIONS
lacZ_4min PGCGROWTHCONDITIONS
lacZ_6min PGCGROWTHCONDITIONS
lacZ_8min PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
mMaple3_0min PGCGROWTHCONDITIONS
mMaple3_10min PGCGROWTHCONDITIONS
mMaple3_15min PGCGROWTHCONDITIONS
mMaple3_1min PGCGROWTHCONDITIONS
mMaple3_2min PGCGROWTHCONDITIONS
mMaple3_4min PGCGROWTHCONDITIONS
mMaple3_6min PGCGROWTHCONDITIONS
mMaple3_8min PGCGROWTHCONDITIONS
MutRep1_0min PGCGROWTHCONDITIONS
MutRep1_10min PGCGROWTHCONDITIONS
MutRep1_15min PGCGROWTHCONDITIONS
MutRep1_20min PGCGROWTHCONDITIONS
MutRep1_2min PGCGROWTHCONDITIONS
MutRep1_4min PGCGROWTHCONDITIONS
MutRep1_6min PGCGROWTHCONDITIONS
MutRep1_8min PGCGROWTHCONDITIONS
MutRep2_0min PGCGROWTHCONDITIONS
MutRep2_10min PGCGROWTHCONDITIONS
MutRep2_15min PGCGROWTHCONDITIONS
MutRep2_20min PGCGROWTHCONDITIONS
MutRep2_2min PGCGROWTHCONDITIONS
MutRep2_4min PGCGROWTHCONDITIONS
MutRep2_6min PGCGROWTHCONDITIONS
MutRep2_8min PGCGROWTHCONDITIONS
neo_0min PGCGROWTHCONDITIONS
neo_10min PGCGROWTHCONDITIONS
neo_15min PGCGROWTHCONDITIONS
neo_1min PGCGROWTHCONDITIONS
neo_2min PGCGROWTHCONDITIONS
neo_4min PGCGROWTHCONDITIONS
neo_6min PGCGROWTHCONDITIONS
neo_8min PGCGROWTHCONDITIONS
phoA_0min PGCGROWTHCONDITIONS
phoA_10min PGCGROWTHCONDITIONS
phoA_15min PGCGROWTHCONDITIONS
phoA_1min PGCGROWTHCONDITIONS
phoA_2min PGCGROWTHCONDITIONS
phoA_4min PGCGROWTHCONDITIONS
phoA_6min PGCGROWTHCONDITIONS
phoA_8min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
time point: 10 min PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
time point: 1 min PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_0min PGCGROWTHCONDITIONS
WTKasRep1_15min PGCGROWTHCONDITIONS
WTKasRep1_20min PGCGROWTHCONDITIONS
WTKasRep1_2min PGCGROWTHCONDITIONS
WTKasRep1_4min PGCGROWTHCONDITIONS
WTKasRep1_6min PGCGROWTHCONDITIONS
WTKasRep1_8min PGCGROWTHCONDITIONS
WTKasRep2_0min PGCGROWTHCONDITIONS
WTKasRep2_10min PGCGROWTHCONDITIONS
WTKasRep2_15min PGCGROWTHCONDITIONS
WTKasRep2_20min PGCGROWTHCONDITIONS
WTKasRep2_2min PGCGROWTHCONDITIONS
WTKasRep2_4min PGCGROWTHCONDITIONS
WTKasRep2_6min PGCGROWTHCONDITIONS
WTKasRep2_8min PGCGROWTHCONDITIONS
WTRep1_0min PGCGROWTHCONDITIONS
WTRep1_10min PGCGROWTHCONDITIONS
WTRep1_15min PGCGROWTHCONDITIONS
WTRep1_20min PGCGROWTHCONDITIONS
WTRep1_2min PGCGROWTHCONDITIONS
WTRep1_4min PGCGROWTHCONDITIONS
WTRep1_6min PGCGROWTHCONDITIONS
WTRep1_8min PGCGROWTHCONDITIONS
WTRep2_0min PGCGROWTHCONDITIONS
WTRep2_10min PGCGROWTHCONDITIONS
WTRep2_15min PGCGROWTHCONDITIONS
WTRep2_20min PGCGROWTHCONDITIONS
WTRep2_2min PGCGROWTHCONDITIONS
WTRep2_4min PGCGROWTHCONDITIONS
WTRep2_6min PGCGROWTHCONDITIONS
WTRep2_8min PGCGROWTHCONDITIONS
cDNA of EPEC strain PGCGROWTHCONDITIONS
CIP2G_00000 PGCGROWTHCONDITIONS
CIP2G_00045 PGCGROWTHCONDITIONS
CIP2G_00090 PGCGROWTHCONDITIONS
CIP2G_00135 PGCGROWTHCONDITIONS
CIP2G_00180 PGCGROWTHCONDITIONS
CIP4G_00000 PGCGROWTHCONDITIONS
CIP4G_00045 PGCGROWTHCONDITIONS
CIP4G_00090 PGCGROWTHCONDITIONS
CIP4G_00135 PGCGROWTHCONDITIONS
CIP4G_00180 PGCGROWTHCONDITIONS
CIPSG_00000 PGCGROWTHCONDITIONS
CIPSG_00045 PGCGROWTHCONDITIONS
CIPSG_00090 PGCGROWTHCONDITIONS
CIPSG_00135 PGCGROWTHCONDITIONS
CIPSG_00180 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA was prepared using the Trizol Reagent and a RiboPure kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol. RNA integrity was assessed using an Agilent 2100 bioanalyser (Agilent, Palo Alto, CA, USA). PGCGROWTHCONDITIONS
strain: EPEC PGCGROWTHCONDITIONS
The scanned images were analyzed using the Feature Extraction Software (Agilent) with default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. PGCGROWTHCONDITIONS
time point: 0 PGCGROWTHCONDITIONS
time point: 135 min PGCGROWTHCONDITIONS
time point: 180 min PGCGROWTHCONDITIONS
time point: 45 min PGCGROWTHCONDITIONS
time point: 90 min PGCGROWTHCONDITIONS
treatment: 2ug PGCGROWTHCONDITIONS
treatment: 4ug PGCGROWTHCONDITIONS
treatment: saline PGCGROWTHCONDITIONS
5' in minimal medium +0.2% glu, 25 ug total RNA PGCGROWTHCONDITIONS
5' in min med +0.2% glu+50ug PGCGROWTHCONDITIONS
5' vs 0' in minimal medium +0.2% glu PGCGROWTHCONDITIONS
60' 10 ug PGCGROWTHCONDITIONS
60' 15 ug PGCGROWTHCONDITIONS
60' + 50 ug PGCGROWTHCONDITIONS
60' 50 ug PGCGROWTHCONDITIONS
60'+50ug PGCGROWTHCONDITIONS
60' in min +.2% glu, 25 ug RNA PGCGROWTHCONDITIONS
60' in minimal medium +0.2% glu, 25 ug total RNA PGCGROWTHCONDITIONS
60' in min med +0.2% glu+50ug PGCGROWTHCONDITIONS
60' vs. 0', 50 ug PGCGROWTHCONDITIONS
60' vs 0' in minimal medium +0.2% glu PGCGROWTHCONDITIONS
60' vs 0' in minimal medium +0.2% glu, II PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli_control condition PGCGROWTHCONDITIONS
Escherichia coli_nickel condition PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_10-WT-Ni-3 PGCGROWTHCONDITIONS
Rodrigue_1-WT-phiNi-1 PGCGROWTHCONDITIONS
Rodrigue_2-WT-Ni-1 PGCGROWTHCONDITIONS
Rodrigue_5-WT-Ni-2 PGCGROWTHCONDITIONS
Rodrigue_6-WT-phiNi-2 PGCGROWTHCONDITIONS
Rodrigue_9-WT-phiNi-3 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
DicF rep1 PGCGROWTHCONDITIONS
DicF rep2 PGCGROWTHCONDITIONS
DicF rep3 PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3) PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: small RNA DicF PGCGROWTHCONDITIONS
protocol: vector control PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3) PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Vector rep1 PGCGROWTHCONDITIONS
Vector rep2 PGCGROWTHCONDITIONS
Vector rep3 PGCGROWTHCONDITIONS
Bacterial cell pellet PGCGROWTHCONDITIONS
Bacterial culture grown overnight at 37C, given 1% sub-culturing till OD at 600nm was 0.4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift PGCGROWTHCONDITIONS
MG1655 G181D NusA BR, treated PGCGROWTHCONDITIONS
MG1655 G181D NusA, treated PGCGROWTHCONDITIONS
MG1655 R258C NusA BR, treated PGCGROWTHCONDITIONS
MG1655 R258C NusA, treated PGCGROWTHCONDITIONS
MG1655 WT NusA BR, control PGCGROWTHCONDITIONS
MG1655 WT NusA, control PGCGROWTHCONDITIONS
plasmid: G181D NusA PGCGROWTHCONDITIONS
plasmid: R258C NusA PGCGROWTHCONDITIONS
plasmid: wild type NusA PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol. PGCGROWTHCONDITIONS
Treated experimental sets transformed with plasmids containing WT PGCGROWTHCONDITIONS
Bacterial cell pellet PGCGROWTHCONDITIONS
Bacterial culture grown overnight at 37C, given 1% sub-culturing till OD at 600nm was 0.4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift PGCGROWTHCONDITIONS
MG1655 G181D NusA BR1, treated PGCGROWTHCONDITIONS
MG1655 G181D NusA BR2, treated PGCGROWTHCONDITIONS
MG1655 R258C NusA BR1, treated PGCGROWTHCONDITIONS
MG1655 R258C NusA BR2, treated PGCGROWTHCONDITIONS
MG1655 WT NusA BR1, control PGCGROWTHCONDITIONS
MG1655 WT NusA BR2, control PGCGROWTHCONDITIONS
plasmid: G181D NusA PGCGROWTHCONDITIONS
plasmid: R258C NuSA PGCGROWTHCONDITIONS
plasmid: wild type NusA PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol. PGCGROWTHCONDITIONS
Treated experimental sets transformed with plasmids containing WT PGCGROWTHCONDITIONS
Bacterial cell pellet PGCGROWTHCONDITIONS
Bacterial culture grown overnight at 37C, given 1% sub-culturing till OD at 600nm was 0.4 PGCGROWTHCONDITIONS
E. coli MG1655, BCM treated-Replicate1 PGCGROWTHCONDITIONS
E. coli MG1655, BCM treated-Replicate2 PGCGROWTHCONDITIONS
E. coli MG1655, Vector control-Replicate1 PGCGROWTHCONDITIONS
E. coli MG1655, Vector control-Replicate2 PGCGROWTHCONDITIONS
E. coli MG1655, WT Rho treated-Replicate1 PGCGROWTHCONDITIONS
E. coli MG1655, WT Rho treated-Replicate2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Images Analysis using Agilent Feature Extraction Software Version 11.5 to obtain raw data.Probe intensities generated from feature extraction raw data were split based on channel type and  analysis was performed. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol. PGCGROWTHCONDITIONS
Treated experimental sets transformed with plasmids containing BCM PGCGROWTHCONDITIONS
treatment: BCM PGCGROWTHCONDITIONS
treatment: vector control PGCGROWTHCONDITIONS
treatment: WT Rho plasmid PGCGROWTHCONDITIONS
Bacterial cell pellet PGCGROWTHCONDITIONS
Bacterial culture grown overnight at 37C, given 1% sub-culturing till OD at 600nm was 0.4 PGCGROWTHCONDITIONS
E. coli MG1655 ∆Rac G324D, treated-Replicate1-mutant PGCGROWTHCONDITIONS
E. coli MG1655 ∆Rac G324D, treated-Replicate2-mutant PGCGROWTHCONDITIONS
E. coli MG1655 ∆Rac N340S, treated-Replicate1-mutant PGCGROWTHCONDITIONS
E. coli MG1655 ∆Rac N340S, treated-Replicate2-mutant PGCGROWTHCONDITIONS
E. coli MG1655 ∆Rac WT, control-Replicate1-Wildtype PGCGROWTHCONDITIONS
E. coli MG1655 ∆Rac WT, control-Replicate2-Wildtype PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: delta-rac PGCGROWTHCONDITIONS
Images Analysis using Agilent Feature Extraction Software Version 11.5 to obtain raw data.Probe intensities generated from feature extraction raw data were split based on channel type and  analysis was performed. PGCGROWTHCONDITIONS
plasmid: G324D Rho mutant PGCGROWTHCONDITIONS
plasmid: N340S Rho mutant PGCGROWTHCONDITIONS
plasmid: WT Rho PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol. PGCGROWTHCONDITIONS
Treated experimental sets transformed with plasmids containing Rho (WT PGCGROWTHCONDITIONS
Adaptor Sequences were removed using fastx_clipper. (http: PGCGROWTHCONDITIONS
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit. PGCGROWTHCONDITIONS
Bacterial Cell Lysates PGCGROWTHCONDITIONS
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1 PGCGROWTHCONDITIONS
Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25 PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Data collapsed using fastx collapser to remove identical sequencing reads (http: PGCGROWTHCONDITIONS
DL4184C_ChIP-seq PGCGROWTHCONDITIONS
DL4201C_ChIP-seq PGCGROWTHCONDITIONS
DL4311C_ChIP-seq PGCGROWTHCONDITIONS
DL4312C_ChIP-seq PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 MG1655 NC000913.3 PGCGROWTHCONDITIONS
genotype: delta_recG263::KanR lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZχ- PGCGROWTHCONDITIONS
genotype: delta_recG263::KanR lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ:: pal246 cynX::GmR  lacIq  lacZχ- PGCGROWTHCONDITIONS
genotype: lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZχ- PGCGROWTHCONDITIONS
genotype: lacZ::χχχ mhpR::χχχ proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ:: pal246 cynX::GmR  lacIq  lacZχ- PGCGROWTHCONDITIONS
Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M PGCGROWTHCONDITIONS
reads were mapped to the E. coli K12 MG1655 (NC000913.3) genome using Novoalign version 2.07  (www.novocraft.com) - Example: (novoalign -f DL4900_clip_clp.fasta -d NC000913.3.nix -r Random > DL4900.novo) PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt files including count data for the whole genome PGCGROWTHCONDITIONS
yPileup was used to generate count data for the whole genome - Example:  pyPileup.py --file_type=novo -f DL4184.novo --tab=NC000913.3.tab --chr=Wholechom.txt -- ignorestrand PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 batch PGCGROWTHCONDITIONS
IAI1 chemostat PGCGROWTHCONDITIONS
IAI1 starvation PGCGROWTHCONDITIONS
IAI1 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
IAI1 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
IAI1 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
IAI1 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
IAI1 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
IAI1 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 batch PGCGROWTHCONDITIONS
MG1655 chemostat PGCGROWTHCONDITIONS
MG1655 starvation PGCGROWTHCONDITIONS
MG1655 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
MG1655 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
MG1655 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
MG1655 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
MG1655 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
MG1655 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
TW09308 batch PGCGROWTHCONDITIONS
TW09308 chemostat PGCGROWTHCONDITIONS
TW09308 starvation PGCGROWTHCONDITIONS
TW09308 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
TW09308 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
TW09308 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
TW09308 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
TW09308 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
TW09308 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
TW11588 batch PGCGROWTHCONDITIONS
TW11588 chemostat PGCGROWTHCONDITIONS
TW11588 starvation PGCGROWTHCONDITIONS
TW11588 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
TW11588 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
TW11588 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
TW11588 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
TW11588 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
TW11588 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described previously (Li et al., 2012; Oh et al., 2011). For ribosome profiling, 200 mL of cell culture were filtered rapidly and the resulting cell pellet was flash-frozen in liquid nitrogen and combined with 650 µL of frozen lysis buffer (10 mM MgCl2, 100mM NH4Cl, 20mM Tris-HCl pH 8.0, 0.1% Nonidet P40, 0.4% Triton X-100, 100 U PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
mRNA-seq 37°C in WT with control plasmid PGCGROWTHCONDITIONS
mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA PGCGROWTHCONDITIONS
mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 [p-CTRL] PGCGROWTHCONDITIONS
strain: MG1655 [p-CUA] PGCGROWTHCONDITIONS
strain: MG1655 [p-CUG] PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
The ribosome footprints and fragmented mRNA were ligated to miRNA cloning linker-1 (IDT) using truncated T4 RNA ligase 2 K227Q. The ligated RNA fragments were reverse transribed using the primer 5Phos PGCGROWTHCONDITIONS
treatment: 1mM IPTG PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
5' linker and poly A-tail removal using READemption PGCGROWTHCONDITIONS
5 ml of cell suspension were added to 0.625 ml of pre-chilled stop solution (5 % phenol PGCGROWTHCONDITIONS
An overnight culture of E. coli O104:H4 strain LB226692 was diluted 1:10,000 in pre-warmed LB medium (10 g PGCGROWTHCONDITIONS
cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng PGCGROWTHCONDITIONS
Escherichia coli O104:H4 PGCGROWTHCONDITIONS
exponentially growing cells PGCGROWTHCONDITIONS
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20 PGCGROWTHCONDITIONS
Fastq to fasta conversion using FastX  FastX (version 0.0.13) PGCGROWTHCONDITIONS
generation of coverage graphs representing the number of pAA plasmid-associated mapped reads per nucleotide using READemption 0.3.7 PGCGROWTHCONDITIONS
Genome_build: NC_018658.1, NC_018659.1, NC_018660.1, NC_018666.1 PGCGROWTHCONDITIONS
mapping of non-rRNA and tRNA reads to E. coli O104:H4 chromosome and plasmids using READemption 0.3.7 and segemehl 0.2.0 PGCGROWTHCONDITIONS
mapping of reads to E. coli O104:H4 rRNAs and tRNAs using READemption 0.3.7 and segemehl 0.2.0 PGCGROWTHCONDITIONS
normalization of graphs to the total number of mapped reads per library using READemption 0.3.7 PGCGROWTHCONDITIONS
origin of isolation: patient with hemolytic uremic syndrome (HUS) PGCGROWTHCONDITIONS
outbreak: 2011 outbreak centered in Northern Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: clinical isolate LB226692 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wig files representing the normalized number of pAA-associated mapped reads per nucleotide. Files contain wiggle-formatted files data for accessions  NC_018658.1, NC_018659.1, NC_018660.1, and NC_018666.1. PGCGROWTHCONDITIONS
TEX-_E. coli O104:H4 PGCGROWTHCONDITIONS
TEX+_E. coli O104:H4 PGCGROWTHCONDITIONS
Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U PGCGROWTHCONDITIONS
Cells were harvested from aerobic and anaerobic cultures of seven E. coli strains grown to an OD600 of 0.6 (exponential phase). Cultures were divided into 10 ml aliquots and were immediately mixed with 0.2 volumes of ice-cold STOP solution (95% ethanol, 5% phenol (pH 4.7)). After 20 min incubation on ice, samples were spun down for 10 min at 4˚C and 7000 x g in a centrifuge. Pellets from one aliquot were gently resuspended in RNAProtect (QIAGEN, Germany) to further stabilize the RNA. Remaining samples were mixed with RNAlater (QIAGEN, Germany) and placed at -80˚C for archival storage. Total RNA was extracted using RNeasy Mini kit (QIAGEN, Germany) and on column DNase treatment following the manufacturers’ instructions. The 23S and 16S rRNAs were removed by subtractive hybridization using the MICROBExpress kit (Ambion, USA) with modifications. Compared with the standard protocol, 50% more capture oligonucleotides and magnetic beads were used. 5S rRNAs (120 nt in length) were removed during the total RNA extraction on column. Specifically, ribosomal depletion on total RNA isolated from the E. coli BL21 (DE3) was performed using RiboZero (Gram Negative Bacteria) kit (Epicenter, USA). RNA samples were stored at -80°C. PGCGROWTHCONDITIONS
Crooks_aero PGCGROWTHCONDITIONS
Crooks_anaero PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS
Gene expression data (3 biological replicates per strain) were analyzed in the statistical software program R (www.r-project.org ) using the EdgeR package (3). Data were normalized using the CQN package, which accounts for both gene length and GC content effects (4). Differentially expressed genes were determined by comparing expression values under anaerobic and aerobic conditions. Those genes with adjusted P values less than 0.01 (i.e., false discovery rate less than 1%) were identified as significantly differentially expressed genes. Finally, gene annotations were automatically made using the biomaRt package (5) together with the annotation files available at the Ensembl database (www.ensembl.org) and gene set enrichment analysis (GSEA) was performed using the piano package (6). All R packages used in this study are available in Bioconductor (www.bioconductor.org). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Crooks PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include gene expresion values for each Sample PGCGROWTHCONDITIONS
The sequencing libraries were constructed using the TruSeq RNA Sample Preparation kit (Illumina Inc., USA). Each library was prepared with RNA isolated from seven E. coli cultures grown in triplicate to an exponential phase under aerobic and anaerobic conditions. RT-PCR was performed with SuperScript® II One-step RT-PCR reagents (Invitrogen, USA). The libraries were sequenced using the Illumina HiSeq2000 platform with a paired-end protocol and read lengths of 50 nt.  The final concentration of DNA and RNA was measured using a Qubit 2.0 Fluorometer (Invitrogen, USA). The integrity of total RNA, DNA contamination, removal of rRNAs and cDNA library validation were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, USA). PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_anoxic (NO3)_glycerol PGCGROWTHCONDITIONS
delta-rnr mutant_anoxic (NO3)_glycerol + propionate PGCGROWTHCONDITIONS
delta-rnr mutant_oxic_glycerol PGCGROWTHCONDITIONS
delta-rnr mutant_oxic_glycerol + propionate PGCGROWTHCONDITIONS
d_rnr NO3 1 PGCGROWTHCONDITIONS
d_rnr NO3 2 PGCGROWTHCONDITIONS
d_rnr NO3 w PGCGROWTHCONDITIONS
d_rnr O2 1 PGCGROWTHCONDITIONS
d_rnr O2 2 PGCGROWTHCONDITIONS
d_rnr O2 w PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038 PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_anoxic (NO3)_glycerol PGCGROWTHCONDITIONS
wild type_anoxic (NO3)_glycerol + propionate PGCGROWTHCONDITIONS
wild type_oxic_glycerol PGCGROWTHCONDITIONS
wild type_oxic_glycerol + propionate PGCGROWTHCONDITIONS
WT NO3 1 PGCGROWTHCONDITIONS
WT NO3 2 PGCGROWTHCONDITIONS
WT NO3 w PGCGROWTHCONDITIONS
WT O2 1 PGCGROWTHCONDITIONS
WT O2 2 PGCGROWTHCONDITIONS
WT O2 w PGCGROWTHCONDITIONS
Control, 0.8%butanol,1.5h,replicate 1 PGCGROWTHCONDITIONS
Control, 0.8%butanol,1.5h,replicate 2 PGCGROWTHCONDITIONS
Control, 0.8%butanol,1.5h,replicate 3 PGCGROWTHCONDITIONS
Control109_0.8%Bu_1.5h_rep1 PGCGROWTHCONDITIONS
Control109_0.8%Bu_1.5h_rep2 PGCGROWTHCONDITIONS
Control109_0.8%Bu_1.5h_rep3 PGCGROWTHCONDITIONS
Data was extracted with Agilent Feature Extraction software 10.7 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. PGCGROWTHCONDITIONS
E. coli strains harboring σ70 mutant B8 and WT were cultured overnight and inoculated (1%) into fresh medium. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Mutant B8_0.8%Bu_1.5h_rep1 PGCGROWTHCONDITIONS
Mutant B8_0.8%Bu_1.5h_rep2 PGCGROWTHCONDITIONS
Mutant B8_0.8%Bu_1.5h_rep3 PGCGROWTHCONDITIONS
Mutant B8, 0.8%butanol,1.5h,replicate 1 PGCGROWTHCONDITIONS
Mutant B8, 0.8%butanol,1.5h,replicate 2 PGCGROWTHCONDITIONS
Mutant B8, 0.8%butanol,1.5h,replicate 3 PGCGROWTHCONDITIONS
n-Butanol (0.8%, v PGCGROWTHCONDITIONS
phenotype: 0.6% n-butanol tolerance PGCGROWTHCONDITIONS
phenotype: 2% n-butanol tolerance PGCGROWTHCONDITIONS
strain: JM109 PGCGROWTHCONDITIONS
Total RNA was extracted using Qiagen RNeasy kit (Hilden, Germany) following manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (QIAGEN, GmBH, Germany). PGCGROWTHCONDITIONS
Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium. PGCGROWTHCONDITIONS
Enteroheamorragic E. coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 10828 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11109 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11117 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11128 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11619 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11711 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11788 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 11845 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 12009 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain 13369 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain ED71 PGCGROWTHCONDITIONS
Genomic DNA from O111 strain PMK5 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 980551 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 980706 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 980938 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 981456 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 981795 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 982243 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 990281 PGCGROWTHCONDITIONS
Genomic DNA from O157 strain 990570 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 11044 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 11368 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 11656 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 12719 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 12929 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 13065 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain 13247 PGCGROWTHCONDITIONS
Genomic DNA from O26 strain ED411 PGCGROWTHCONDITIONS
Genomic DNA was purified using the Genomic-tip 100 PGCGROWTHCONDITIONS
O103 no.1 (strain 10828) replicate 1 PGCGROWTHCONDITIONS
O103 no.1 (strain 10828) replicate 2 PGCGROWTHCONDITIONS
O103 no.2 (strain 11117) replicate 1 PGCGROWTHCONDITIONS
O103 no.2 (strain 11117) replicate 2 PGCGROWTHCONDITIONS
O103 no.3 (strain 11711) replicate 1 PGCGROWTHCONDITIONS
O103 no.3 (strain 11711) replicate 2 PGCGROWTHCONDITIONS
O103 no.4 (strain 11845) replicate 1 PGCGROWTHCONDITIONS
O103 no.4 (strain 11845) replicate 2 PGCGROWTHCONDITIONS
O103 no.5 (strain 12009) replicate 1 PGCGROWTHCONDITIONS
O103 no.5 (strain 12009) replicate 2 PGCGROWTHCONDITIONS
O103 no.6 (strain PMK5) replicate 1 PGCGROWTHCONDITIONS
O103 no.6 (strain PMK5) replicate 2 PGCGROWTHCONDITIONS
O111 no.1 (strain 11109) replicate 1 PGCGROWTHCONDITIONS
O111 no.1 (strain 11109) replicate 2 PGCGROWTHCONDITIONS
O111 no.2 (strain 11128) replicate 1 PGCGROWTHCONDITIONS
O111 no.2 (strain 11128) replicate 2 PGCGROWTHCONDITIONS
O111 no.3 (strain 11619) replicate 1 PGCGROWTHCONDITIONS
O111 no.3 (strain 11619) replicate 2 PGCGROWTHCONDITIONS
O111 no.4 (strain 11788) replicate 1 PGCGROWTHCONDITIONS
O111 no.4 (strain 11788) replicate 2 PGCGROWTHCONDITIONS
O111 no.5 (strain 13369) replicate 1 PGCGROWTHCONDITIONS
O111 no.5 (strain 13369) replicate 2 PGCGROWTHCONDITIONS
O111 no.6 (strain ED71) replicate 1 PGCGROWTHCONDITIONS
O111 no.6 (strain ED71) replicate 2 PGCGROWTHCONDITIONS
O157 no.2 (strain 980938) replicate 1 PGCGROWTHCONDITIONS
O157 no.2 (strain 980938) replicate 2 PGCGROWTHCONDITIONS
O157 no.3 (strain 980706) replicate 1 PGCGROWTHCONDITIONS
O157 no.3 (strain 980706) replicate 2 PGCGROWTHCONDITIONS
O157 no.4 (strain 990281) replicate 1 PGCGROWTHCONDITIONS
O157 no.4 (strain 990281) replicate 2 PGCGROWTHCONDITIONS
O157 no.5 (strain 980551) replicate 1 PGCGROWTHCONDITIONS
O157 no.5 (strain 980551) replicate 2 PGCGROWTHCONDITIONS
O157 no.6 (strain 990570) replicate 1 PGCGROWTHCONDITIONS
O157 no.6 (strain 990570) replicate 2 PGCGROWTHCONDITIONS
O157 no.7 (strain 981456) replicate 1 PGCGROWTHCONDITIONS
O157 no.7 (strain 981456) replicate 2 PGCGROWTHCONDITIONS
O157 no.8 (strain 982243) replicate 1 PGCGROWTHCONDITIONS
O157 no.8 (strain 982243) replicate 2 PGCGROWTHCONDITIONS
O157 no.9 (strain 981795) replicate 1 PGCGROWTHCONDITIONS
O157 no.9 (strain 981795) replicate 2 PGCGROWTHCONDITIONS
O157 strain Sakai PGCGROWTHCONDITIONS
O26 no.1 (strain 11044) replicate 1 PGCGROWTHCONDITIONS
O26 no.1 (strain 11044) replicate 2 PGCGROWTHCONDITIONS
O26 no.2 (strain 11368) replicate 1 PGCGROWTHCONDITIONS
O26 no.2 (strain 11368) replicate 2 PGCGROWTHCONDITIONS
O26 no.3 (strain 11656) replicate 1 PGCGROWTHCONDITIONS
O26 no.3 (strain 11656) replicate 2 PGCGROWTHCONDITIONS
O26 no.4 (strain 12719) replicate 1 PGCGROWTHCONDITIONS
O26 no.4 (strain 12719) replicate 2 PGCGROWTHCONDITIONS
O26 no.5 (strain 12929) replicate 1 PGCGROWTHCONDITIONS
O26 no.5 (strain 12929) replicate 2 PGCGROWTHCONDITIONS
O26 no.6 (strain 13065) replicate 1 PGCGROWTHCONDITIONS
O26 no.6 (strain 13065) replicate 2 PGCGROWTHCONDITIONS
O26 no.7 (strain 13247) replicate 1 PGCGROWTHCONDITIONS
O26 no.7 (strain 13247) replicate 2 PGCGROWTHCONDITIONS
O26 no.8 (strain ED411) replicate 1 PGCGROWTHCONDITIONS
O26 no.8 (strain ED411) replicate 2 PGCGROWTHCONDITIONS
Spots with reference signal intensities lower than the local background (LBG)  plus 5 standard deviations or with some spotting abnormalities were removed from analysis. Signal intensities of other spots were corrected by subtracting the LBG. PGCGROWTHCONDITIONS
172mM SCFA replicate 1 PGCGROWTHCONDITIONS
172mM SCFA replicate 2 PGCGROWTHCONDITIONS
30mM SCFA replicate 1 PGCGROWTHCONDITIONS
30mM SCFA replicate 2 PGCGROWTHCONDITIONS
30mM SCFA replicate 3 PGCGROWTHCONDITIONS
30mM SCFA replicate 4 PGCGROWTHCONDITIONS
e. coli subset: enterohemorrhagic E.coli PGCGROWTHCONDITIONS
enterohemorrhagic E. coli_172mM short chain fatty acid mix PGCGROWTHCONDITIONS
enterohemorrhagic E. coli_30mM short chain fatty acid mix PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Images were quantified and normalized using extraction protocol GE2_107_Sept09 and Agilent Feature Extraction Software (version 10.7.3.1). PGCGROWTHCONDITIONS
N172-1 PGCGROWTHCONDITIONS
N172-2 PGCGROWTHCONDITIONS
N30-1 PGCGROWTHCONDITIONS
N30-2 PGCGROWTHCONDITIONS
N30-3 PGCGROWTHCONDITIONS
N30-4 PGCGROWTHCONDITIONS
overnight bacterial culture in Luria Broth at 37C with shaking PGCGROWTHCONDITIONS
overnight culture subcultured in either of the SCFA mixes (or the sodium chloride controls) at 37C, static with 5%CO2 to OD600 of 1 PGCGROWTHCONDITIONS
total RNA extracted using Trizol Extraction Protocol PGCGROWTHCONDITIONS
treated with: 172mM NaCl PGCGROWTHCONDITIONS
treated with: 172mM short chain fatty acid mix PGCGROWTHCONDITIONS
treated with: 30mM NaCl PGCGROWTHCONDITIONS
treated with: 30mM short chain fatty acid mix PGCGROWTHCONDITIONS
Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or LB PGCGROWTHCONDITIONS
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland PGCGROWTHCONDITIONS
Escherichia coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For REC-Seq (restriction enzyme cleavage–sequencing) 1 ug of genomic DNA from C.  crescentus NA1000 and S. meliloti Rm2011 was cleaved with HinfI, a blocked (5’biotinylated)  specific adaptor was ligated to the ends and the ligated fragments were then sheared to an average size  of 150-400 bp (Fasteris SA, Geneva, CH). Illumina adaptors were then ligated to the sheared ends  followed by deep-sequencing using a Hi-Seq Illumina sequencer, and the (50 bp single end) reads  were quality controlled with FastQC (http: PGCGROWTHCONDITIONS
genome build: NC_000913.3 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
GHA507 PGCGROWTHCONDITIONS
Library strategy: REC-Seq PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab delimited text files, with feature annotation, REC_seq score, gene name and description PGCGROWTHCONDITIONS
To remove contaminating sequences, the reads were split according to the HinfI consensus motif (5’-  G^ANTC-3’) considered as a barcode sequence using fastx_toolkit  (http: PGCGROWTHCONDITIONS
cy_a4 PGCGROWTHCONDITIONS
cy_b4 PGCGROWTHCONDITIONS
cyc1 PGCGROWTHCONDITIONS
cyc2 PGCGROWTHCONDITIONS
cyc3 PGCGROWTHCONDITIONS
cyc4 PGCGROWTHCONDITIONS
cyd1 PGCGROWTHCONDITIONS
cyd2 PGCGROWTHCONDITIONS
cyd3 PGCGROWTHCONDITIONS
cyd4 PGCGROWTHCONDITIONS
dnaC genomic DNA, Sau3A, 2 ug PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
reference 0', min +.2% glu, 25 ug RNA PGCGROWTHCONDITIONS
tnaA2trpA46PR9 vs. tnaA2, W3110 min PGCGROWTHCONDITIONS
tnaA2trpA46PR9, W3110 min , 30 ug total PGCGROWTHCONDITIONS
tnaA2trpR2 vs. tnaA2, W3110 min +Trp 50ug PGCGROWTHCONDITIONS
tnaA2trpR2, W3110 min +Trp 50ug PGCGROWTHCONDITIONS
tnaA2,W3110 min,30 ug total PGCGROWTHCONDITIONS
tnaA2,W3110 minimal +Trp 50ug PGCGROWTHCONDITIONS
tnaA2,W3110 min +Trp 50ug PGCGROWTHCONDITIONS
trpEA2trpR2 vs. trpEA2, W3110 min +Trp 50ug PGCGROWTHCONDITIONS
trpEA2trpR2, W3110 min +Trp 50ug PGCGROWTHCONDITIONS
trpEA2,W3110 min +Trp 50ug PGCGROWTHCONDITIONS
trpR2+50ug PGCGROWTHCONDITIONS
trpR2tnaA2,W3110 minimal +Trp 50ug PGCGROWTHCONDITIONS
trpR2tnaA2,W3110 min +Trp 50ug PGCGROWTHCONDITIONS
trpR2 +trp vs. -trp, min+.2%glucose, W3110 PGCGROWTHCONDITIONS
trpR2 vs. wt, min+.2%glucose, W3110 PGCGROWTHCONDITIONS
W3110 trpR2,min+.2%glucose, 30 ug RNA PGCGROWTHCONDITIONS
W3110 trpR2 -trp, 30 ug total RNA PGCGROWTHCONDITIONS
W3110 trpR2+trp, 30 ug total RNA PGCGROWTHCONDITIONS
W3110 wt, min+.2%glucose, 30 ug RNA PGCGROWTHCONDITIONS
W3110 wt-trp, 30 ug total RNA PGCGROWTHCONDITIONS
W3110 wt+trp, 30 ug total RNA PGCGROWTHCONDITIONS
wt+50ug PGCGROWTHCONDITIONS
wt +trp vs. -trp, min+.2%glucose, W3110 PGCGROWTHCONDITIONS
At each time point, 15 ml of each culture was mixed with 30 ml of RNAprotect Bacteria Reagent (Qiagen), vortexed for 5s, incubated for 5 min at room temperature, and centrifuged for 10 min at 5000g.  The pellet was processed using a Qiagen RNeasy Midi kit with on-column DNase digestion using Qiagen DNase.  The final elution of RNA from the column was with 160 μl RNase-free water. PGCGROWTHCONDITIONS
At OD630nm = 0.1, the cultures were filtered through 47-mm diameter polycarbonate membrane filter (0.4 µm pore size; Millipore), washed with the same medium without hypoxanthine (Hx), and then resuspended at the same cell density (OD630 = 0.1) in the medium without Hx, and growth was continued as before.  The OD630 was followed closely during the next two hours, and the cells were periodically diluted with fresh, pre-warmed medium without Hx to keep OD between values 0.1 and 0.3 (low-dilution protocol).  Samples were taken for microarray analysis (see below) at 0, 15, 30, 45, 60 and 120 minutes.  In a parallel procedure, the optA1 gpt double mutant was also followed in a near-identical manner using a more highly diluted culture over a six-hour incubation period in the absence of hypoxanthine (high-dilution protocol).  The effectiveness of the latter treatment was followed microscopically by observing the extensive cellular filamentation associated with dGTP starvation. PGCGROWTHCONDITIONS
control strain w PGCGROWTHCONDITIONS
control strain with hypoxanthine PGCGROWTHCONDITIONS
Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
gpt_0_Hx Rep1 PGCGROWTHCONDITIONS
gpt_0_Hx Rep2 PGCGROWTHCONDITIONS
gpt_0_Hx Rep3 PGCGROWTHCONDITIONS
gpt_120 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
gpt_120 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
gpt_120 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
gpt_15 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
gpt_15 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
gpt_15 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
gpt_30 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
gpt_30 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
gpt_30 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
gpt_45 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
gpt_45 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
gpt_45 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
gpt_60 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
gpt_60 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
gpt_60 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
gpt strain w PGCGROWTHCONDITIONS
gpt strain with hypoxanthine PGCGROWTHCONDITIONS
optA1_0_Hx Rep1 PGCGROWTHCONDITIONS
optA1_0_Hx Rep2 PGCGROWTHCONDITIONS
optA1_0_Hx Rep3 PGCGROWTHCONDITIONS
optA1_120 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_120 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_120 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_15 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_15 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_15 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_30 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_30 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_30 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_45 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_45 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_45 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_60 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_60 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_60 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_0_Hx Rep1 PGCGROWTHCONDITIONS
optA1_gpt_0_Hx Rep2 PGCGROWTHCONDITIONS
optA1_gpt_0_Hx Rep3 PGCGROWTHCONDITIONS
optA1_gpt_120 (High Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_120 (High Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_120 (High Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_120 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_120 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_120 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_15 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_15 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_15 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_180 (High Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_180 (High Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_180 (High Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_240 (High Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_240 (High Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_240 (High Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_300 (High Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_300 (High Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_300 (High Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_30 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_30 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_30 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_360 (High Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_360 (High Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_360 (High Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_360 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_360 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_360 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_45 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_45 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_45 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1_gpt_60 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
optA1_gpt_60 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
optA1_gpt_60 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
optA1 gpt strain w PGCGROWTHCONDITIONS
optA1 gpt strain with hypoxanthine PGCGROWTHCONDITIONS
optA1 strain w PGCGROWTHCONDITIONS
optA1 strain with hypoxanthine PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
The strains were grown exponentially (after initiation by a 1,000-fold dilution from overnight cultures) for ~5 generations at 37°C in Vogel-Bonner (VB) minimal medium supplemented with glucose (0.4%), pantothenic acid (5 µg PGCGROWTHCONDITIONS
WT_0_Hx Rep1 PGCGROWTHCONDITIONS
WT_0_Hx Rep2 PGCGROWTHCONDITIONS
WT_0_Hx Rep3 PGCGROWTHCONDITIONS
WT_120 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
WT_120 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
WT_120 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
WT_15 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
WT_15 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
WT_15 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
WT_30 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
WT_30 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
WT_30 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
WT_45 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
WT_45 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
WT_45 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
WT_60 (Low Dilution) Rep1 PGCGROWTHCONDITIONS
WT_60 (Low Dilution) Rep2 PGCGROWTHCONDITIONS
WT_60 (Low Dilution) Rep3 PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol PGCGROWTHCONDITIONS
Clindamycin_replicate_1 PGCGROWTHCONDITIONS
Clindamycin_replicate_2 PGCGROWTHCONDITIONS
Clindamycin_replicate_3 PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Erythromycin_replicate_1 PGCGROWTHCONDITIONS
Erythromycin_replicate_2 PGCGROWTHCONDITIONS
Erythromycin_replicate_3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: clindamycin PGCGROWTHCONDITIONS
treatment: erythromycin PGCGROWTHCONDITIONS
treatment: untreated PGCGROWTHCONDITIONS
Untreated_replicate_1 PGCGROWTHCONDITIONS
Untreated_replicate_2 PGCGROWTHCONDITIONS
Untreated_replicate_3 PGCGROWTHCONDITIONS
Aerobic 1 PGCGROWTHCONDITIONS
Aerobic 2 PGCGROWTHCONDITIONS
Aerobic 3 PGCGROWTHCONDITIONS
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1 PGCGROWTHCONDITIONS
Anaerobic 1 PGCGROWTHCONDITIONS
Anaerobic 3 PGCGROWTHCONDITIONS
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
Cultured cells PGCGROWTHCONDITIONS
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
growth environment: Aerobic PGCGROWTHCONDITIONS
growth environment: Anaerobic PGCGROWTHCONDITIONS
growth phase: Stationary phase PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
strain: REL4536 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
DMSO_0min_rep1 PGCGROWTHCONDITIONS
DMSO_0min_rep2 PGCGROWTHCONDITIONS
DMSO_0min_rep3 PGCGROWTHCONDITIONS
DMSO_60min_rep1 PGCGROWTHCONDITIONS
DMSO_60min_rep2 PGCGROWTHCONDITIONS
DMSO_60min_rep3 PGCGROWTHCONDITIONS
DMSO_60min_rep4 PGCGROWTHCONDITIONS
DMSO treatment, 0 min, replicate 1 PGCGROWTHCONDITIONS
DMSO treatment, 0 min, replicate 2 PGCGROWTHCONDITIONS
DMSO treatment, 0 min, replicate 3 PGCGROWTHCONDITIONS
DMSO treatment, 60 min, replicate 1 PGCGROWTHCONDITIONS
DMSO treatment, 60 min, replicate 2 PGCGROWTHCONDITIONS
DMSO treatment, 60 min, replicate 3 PGCGROWTHCONDITIONS
DMSO treatment, 60 min, replicate 4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Raw Microarray data evaluation including preprocessing, normalization, grouping the differentially expressed genes and statistical analyses with Moderated T-test and Bonferroni FWER was carried out with GeneSpring 13.0 Software. PGCGROWTHCONDITIONS
Roemerine_0min_rep1 PGCGROWTHCONDITIONS
Roemerine_0min_rep2 PGCGROWTHCONDITIONS
Roemerine_0min_rep3 PGCGROWTHCONDITIONS
Roemerine_60min_rep1 PGCGROWTHCONDITIONS
Roemerine_60min_rep2 PGCGROWTHCONDITIONS
Roemerine_60min_rep3 PGCGROWTHCONDITIONS
(-)-Roemerine treatment, 0 min, replicate 1 PGCGROWTHCONDITIONS
(-)-Roemerine treatment, 0 min, replicate 2 PGCGROWTHCONDITIONS
(-)-Roemerine treatment, 0 min, replicate 3 PGCGROWTHCONDITIONS
(-)-Roemerine treatment, 60 min, replicate 1 PGCGROWTHCONDITIONS
(-)-Roemerine treatment, 60 min, replicate 2 PGCGROWTHCONDITIONS
(-)-Roemerine treatment, 60 min, replicate 3 PGCGROWTHCONDITIONS
strain: TB1 PGCGROWTHCONDITIONS
The pre-culture was the overnight propagated cells in 5 ml of LB medium at 37ºC and 180 rpm. The main bacterial culture was prepared by 1% inoculation from pre-culture when optical densities at 600 nm (i.e., OD600) reached 0.7. Growth was achieved in 50 ml of LB medium. PGCGROWTHCONDITIONS
Total RNA extraction was carried out based on the protocols given in the manual of QIAGEN - RNAprotect Bacteria Reagent Handbook, QIAGEN - RNeasy Mini Kit and QIAGEN - RNase-free DNase set. The concentration of each RNA sample was measured by Qubit® RNA BR Assay Kit (Invitrogen). PGCGROWTHCONDITIONS
When OD600 of the culture reached 0.54±0.06, cells were treated with 100 µg PGCGROWTHCONDITIONS
0 min Nov0 ug PGCGROWTHCONDITIONS
0 min Nov500 ug PGCGROWTHCONDITIONS
1005 fork-blocking strain induced for Tus PGCGROWTHCONDITIONS
1005 fork-blocking strain induced for Tus: fork5_2 PGCGROWTHCONDITIONS
1005 fork-blocking strain induced for Tus: fork5_3 PGCGROWTHCONDITIONS
1005, LB + 0.2% glucose (tus repressed) PGCGROWTHCONDITIONS
1005, LB + 0.4% arabinose, 2.5 hr (tus induced) PGCGROWTHCONDITIONS
1005, LB + 0.4% arabinose, 3.5 hr (tus induced) PGCGROWTHCONDITIONS
1005, LB + 0.4% arabinose, 90' (tus induced) PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: mfd- PGCGROWTHCONDITIONS
genotype: Mfd++ PGCGROWTHCONDITIONS
genotype: Wildtype PGCGROWTHCONDITIONS
genotype: Wildtype with vector PGCGROWTHCONDITIONS
mfd_1 PGCGROWTHCONDITIONS
MFD++_1 PGCGROWTHCONDITIONS
mfd_2 PGCGROWTHCONDITIONS
MFD++_2 PGCGROWTHCONDITIONS
mfd_3 PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
MG1655_1 PGCGROWTHCONDITIONS
MG1655_2 PGCGROWTHCONDITIONS
MG1655_3 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655_vector_1 PGCGROWTHCONDITIONS
MG1655_vector_2 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium PGCGROWTHCONDITIONS
bacteria grown in LB in vitro PGCGROWTHCONDITIONS
bacteria harvested from blood of chickens PGCGROWTHCONDITIONS
condition: in vitro PGCGROWTHCONDITIONS
condition: in vivo PGCGROWTHCONDITIONS
E058 in vitro, biological rep1 PGCGROWTHCONDITIONS
E058 in vitro, biological rep2 PGCGROWTHCONDITIONS
E058 in vivo, biological rep1 PGCGROWTHCONDITIONS
E058 in vivo, biological rep2 PGCGROWTHCONDITIONS
E058 in vivo, biological rep3 PGCGROWTHCONDITIONS
Escherichia coli APEC O2 PGCGROWTHCONDITIONS
strain: O2 PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. PGCGROWTHCONDITIONS
The in vitro bacterial samples were harvested by centrifugation (5000 × g, 10 min, 4 °C) and the pellet was frozen at −70 °C until RNA extraction. The in vivo bacterial samples were harvested with two-step centrifugation. We first centrifuged the collected anticoagulated blood samples at low speed to remove the abundant red and white blood cells and collected the upper serum layer. We then used high-speed centrifugation to precipitate the bacteria from the serum. PGCGROWTHCONDITIONS
To prepare the in vitro samples, APEC strain E058 was grown statically at 37 °C in 10 mL of LB broth until the absorbance at 600 nm (A600) reached 0.4. To prepare the in vivo samples, the bacteria was harvested from cardiac blood  in 1-day-old chickens at 5 hours post infection. PGCGROWTHCONDITIONS
Total RNA from both the in vitro and in vivo samples of APEC E058 was extracted with the RNAiso Plus kit (Takara, Dalian, China) and further purified with NucleoSpin RNA Clean-up (Macherey-Nagel, Germany), according to the manufacturers’ instructions. PGCGROWTHCONDITIONS
1 min Nov0 ug PGCGROWTHCONDITIONS
1 min Nov500 ug PGCGROWTHCONDITIONS
20 min Nov0 ug PGCGROWTHCONDITIONS
20 min Nov500 ug PGCGROWTHCONDITIONS
20 min Nov50 ug PGCGROWTHCONDITIONS
1.1A PGCGROWTHCONDITIONS
1.1A_Earth_25 PGCGROWTHCONDITIONS
1.2A PGCGROWTHCONDITIONS
1.2A_Space_25 PGCGROWTHCONDITIONS
1.3A PGCGROWTHCONDITIONS
1.3A_Earth_25 PGCGROWTHCONDITIONS
1.4A PGCGROWTHCONDITIONS
1.4A_Space_25 PGCGROWTHCONDITIONS
1.5A PGCGROWTHCONDITIONS
1.5A_Earth_50 PGCGROWTHCONDITIONS
1.6A PGCGROWTHCONDITIONS
1.6A_Space_50 PGCGROWTHCONDITIONS
17.1A PGCGROWTHCONDITIONS
17.1A_Space_25 PGCGROWTHCONDITIONS
17.2A PGCGROWTHCONDITIONS
17.2A_Earth_25 PGCGROWTHCONDITIONS
17.3A PGCGROWTHCONDITIONS
17.3A_Space_25 PGCGROWTHCONDITIONS
17.4A PGCGROWTHCONDITIONS
17.4A_Earth_25 PGCGROWTHCONDITIONS
17.5A PGCGROWTHCONDITIONS
17.5A_Space_50 PGCGROWTHCONDITIONS
17.6A PGCGROWTHCONDITIONS
17.6A_Space_50 PGCGROWTHCONDITIONS
17.8A PGCGROWTHCONDITIONS
17.8A_Earth_50 PGCGROWTHCONDITIONS
1.7A PGCGROWTHCONDITIONS
1.7A_Earth_50 PGCGROWTHCONDITIONS
18.2A PGCGROWTHCONDITIONS
18.2A_Earth_75 PGCGROWTHCONDITIONS
18.3A PGCGROWTHCONDITIONS
18.3A_Space_75 PGCGROWTHCONDITIONS
18.4A PGCGROWTHCONDITIONS
18.4A_Earth_75 PGCGROWTHCONDITIONS
2.1A PGCGROWTHCONDITIONS
2.1A_Earth_75 PGCGROWTHCONDITIONS
2.3A PGCGROWTHCONDITIONS
2.3A_Earth_75 PGCGROWTHCONDITIONS
2.4A PGCGROWTHCONDITIONS
2.4A_Space_75 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
2 min Nov10 ug PGCGROWTHCONDITIONS
2 min Nov2 ug PGCGROWTHCONDITIONS
2 min Nov5 ug PGCGROWTHCONDITIONS
15 min after turning off oxygen PGCGROWTHCONDITIONS
2003, PNAS). To minimize the effect of such contributions, microarray data were PGCGROWTHCONDITIONS
25 min after turning off oxygen PGCGROWTHCONDITIONS
2 min after turning off oxygen PGCGROWTHCONDITIONS
55 min after turning off oxygen PGCGROWTHCONDITIONS
5 min after turning off oxygen PGCGROWTHCONDITIONS
5 min after turning off oxygen first replicate PGCGROWTHCONDITIONS
(B), column (X), and row (Y) number, red foreground (f_r) and background (b_r), green PGCGROWTHCONDITIONS
completely aerobic conditions PGCGROWTHCONDITIONS
corresponding to the same tip. Finally, all the log ratios of the same gene from each slide PGCGROWTHCONDITIONS
E coli, 0 min PGCGROWTHCONDITIONS
E coli, 15 min PGCGROWTHCONDITIONS
E coli, 25 min PGCGROWTHCONDITIONS
E coli, 25 min after turning off oxygen PGCGROWTHCONDITIONS
Ecoli, 2 min PGCGROWTHCONDITIONS
E coli, 2 min after turning off oxygen PGCGROWTHCONDITIONS
E coli, 35 min PGCGROWTHCONDITIONS
E coli, 35 min after turning off oxygen PGCGROWTHCONDITIONS
E coli, 45 min PGCGROWTHCONDITIONS
E coli, 45 min after turning off oxygen PGCGROWTHCONDITIONS
E coli, 55 min PGCGROWTHCONDITIONS
E coli, 5 min PGCGROWTHCONDITIONS
Ecoli, 5 min after turning off oxygen PGCGROWTHCONDITIONS
E coli, 5 min after turning off oxygen first replicate PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_0min PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_15min PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_25min_rep1 PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_25min_rep2 PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_2min PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_35min PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_45min PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_55min_rep1 PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_55min_rep2 PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_5min_Rep1 PGCGROWTHCONDITIONS
ecoli_aerobicanaerobic_5min_rep2 PGCGROWTHCONDITIONS
Ecoli, completely aerobic conditions PGCGROWTHCONDITIONS
E coli, immediately after turning off oxygen PGCGROWTHCONDITIONS
Epicentre MasterPure RNA isolation Kit, Madison, WI PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
fluorescent labeling and hybridization and scanning of the microarray images (Balazsi et al. PGCGROWTHCONDITIONS
foreground and background, and the median Cy3 (green) foreground and background PGCGROWTHCONDITIONS
foreground (f_g) and background (b_g) intensity. The position of each probe within a block, PGCGROWTHCONDITIONS
further analysis if the foreground intensity of less than 50% of the pixels within the spot PGCGROWTHCONDITIONS
Immediately after turning off oxygen PGCGROWTHCONDITIONS
infinity. These values were eliminated using the find, imag, and isfinite functions in Matlab. PGCGROWTHCONDITIONS
in Microsoft Excel, containing the following information for each of the 14,352 entries: block PGCGROWTHCONDITIONS
intensities, respectively. In some cases, when the intensity of the background was higher PGCGROWTHCONDITIONS
Next, data were normalized, by averaging the log ratios resulting from all spots printed by a PGCGROWTHCONDITIONS
normalized as described before (Tong et al. 2004 BBRC). Briefly, spots were excluded from PGCGROWTHCONDITIONS
of (F_r-B_r) PGCGROWTHCONDITIONS
originate during array printing, as well as during the collection and processing of samples, PGCGROWTHCONDITIONS
P is defined by the pair of integers (X,Y). Log ratios were defined as the base 10 logarithm PGCGROWTHCONDITIONS
print tip, and subtracting the resulting average from all the individual log ratios PGCGROWTHCONDITIONS
than or equal to the intensity of the foreground, the resulting log ratios became complex or PGCGROWTHCONDITIONS
Two color cDNA microarray data are never devoid of spurious technical contributions that PGCGROWTHCONDITIONS
Two color cDNA microarray data are never devoid of spurious technical contributions that originate during array printing, as well as during the collection and processing of samples, fluorescent labeling and hybridization and scanning of the microarray images (Balazsi et al. 2003, PNAS).  To minimize the effect of such contributions, microarray data were normalized as described before (Tong et al. 2004 BBRC). Briefly, spots were excluded from further analysis if the foreground intensity of less than 50% of the pixels within the spot were above 2 standard deviations of the background. We generated expression data tables in Microsoft Excel, containing the following information for each of the 14,352 entries: block (B), column (X), and row (Y) number, red foreground (f_r) and background (b_r), green foreground (f_g) and background (b_g) intensity. The position of each probe within a block, P is defined by the pair of integers (X,Y). Log ratios were defined as the base 10 logarithm of (F_r-B_r) PGCGROWTHCONDITIONS
were above 2 standard deviations of the background. We generated expression data tables PGCGROWTHCONDITIONS
were averaged and listed in a new file. PGCGROWTHCONDITIONS
40 min Nov10 ug PGCGROWTHCONDITIONS
40 min Nov2 ug PGCGROWTHCONDITIONS
40 min Nov5 ug PGCGROWTHCONDITIONS
CAR005 PGCGROWTHCONDITIONS
CAR005 strain PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
G4H14 PGCGROWTHCONDITIONS
G4H14 strain PGCGROWTHCONDITIONS
Genome_build: ASM1938v1 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
IspG1 PGCGROWTHCONDITIONS
IspG1 strain PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
Single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm for 5 h. PGCGROWTHCONDITIONS
strain: CAR005 PGCGROWTHCONDITIONS
strain: G4H14 PGCGROWTHCONDITIONS
strain: IspG1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
E.coli cells PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ATCC8739 PGCGROWTHCONDITIONS
growth condition: normal condtion (5% w PGCGROWTHCONDITIONS
growth condition: osmotic stress condtion (12% w PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
NZ502_12%Glu PGCGROWTHCONDITIONS
NZ502_5%Glu PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
strain: NZ-502 (RpoB mutant) PGCGROWTHCONDITIONS
strain: Suc-T110 (parental strain) PGCGROWTHCONDITIONS
SucT110_12%Glu PGCGROWTHCONDITIONS
SucT110_5%Glu PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample . PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: K12 - MG1655 PGCGROWTHCONDITIONS
growth condition: Exponential + O2 PGCGROWTHCONDITIONS
growth condition: Static + O2 PGCGROWTHCONDITIONS
library strategy: ChIP-exo PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
Samples 931, 933, 935 and 937 were aligned with bowtie (V 1.1.2) with parameters  --wrapper basic-0 -q -m 1 -l 55 -k 1 -5 3 -3 40 --best -S -p 24, and samples 1311, 1314, 1317 and 1320 were aligned with bowtie (V 1.1.2) with paramters --wrapper basic-0 -q -m 1 -v 2 --best -p 24 -S PGCGROWTHCONDITIONS
Sig70 in E. coli_exponential aerobic growth_no rifampicin PGCGROWTHCONDITIONS
Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 1 (run 299) PGCGROWTHCONDITIONS
Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 1 (run 423) PGCGROWTHCONDITIONS
Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 2 (run 299) PGCGROWTHCONDITIONS
Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 2 (run 423) PGCGROWTHCONDITIONS
Sig70 in E. coli_exponential aerobic growth_rifampicin PGCGROWTHCONDITIONS
Sig70 in E. coli, exponential aerobic growth, rifampicin applied for 20 minutes, replicate 1 (run 423) PGCGROWTHCONDITIONS
Sig70 in E. coli, exponential aerobic growth, rifampicin applied for 20 minutes, replicate 2 (run 423) PGCGROWTHCONDITIONS
Sig70 in E. coli_static aerobic growth_no rifampicin PGCGROWTHCONDITIONS
Sig70 in E. coli, static aerobic growth, no rifampicin applied replicate 1 (run 299) PGCGROWTHCONDITIONS
Sig70 in E. coli, static aerobic growth, no rifampicin applied replicate 2 (run 299) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Each wig file contains the alignd reads of each ChIP-exo sample. PGCGROWTHCONDITIONS
The ChIP-exo experiments were generated by following the steps presented by Rhee and Pugh, 2011. PGCGROWTHCONDITIONS
The samples were sonicated for a total of 16 minutes and 50 uL protein A PGCGROWTHCONDITIONS
treated with: none PGCGROWTHCONDITIONS
treated with: Rifampicin for 20 minutes PGCGROWTHCONDITIONS
E. coli W3110 PGCGROWTHCONDITIONS
E. coli W3110 expressing PCK PGCGROWTHCONDITIONS
E. coli W3110 expressing ppc PGCGROWTHCONDITIONS
E. coli W3110 expressing ppc at LB-GlC medium, D=0.1 h-1 PGCGROWTHCONDITIONS
E. coli W3110 grown at glucose-minimal medium (IPTG induction) in early log phase (u=0.25 h-1) PGCGROWTHCONDITIONS
E. coli W3110 grown at LB-glucose medium (IPTG induction) in chemostat (D=0.1 h-1) PGCGROWTHCONDITIONS
E. coli W3110 (KCTC 2223) PGCGROWTHCONDITIONS
E. coli W3110 (KCTC 2223)  PGCGROWTHCONDITIONS
E. coli W3110 (KCTC 2223) at LB-GlC medium, D=0.1 h-1 PGCGROWTHCONDITIONS
E. coli W3110 with glucose-minimal medium (IPTG induced) at early log phase (u=0.25) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
PCK_glucose-minimal medium_early log phase PGCGROWTHCONDITIONS
PCK_LB-GlC medium_D=0.1 h-1 PGCGROWTHCONDITIONS
PPC_glucose-minimal medium_early log phase PGCGROWTHCONDITIONS
PPC_LB-GlC medium_D=0.1 h-1 PGCGROWTHCONDITIONS
Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios.  PGCGROWTHCONDITIONS
Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios. Logged gene expression ratios were normalized by LOWESS regression (Yang et al., 2002) using the GeneSpring GX 7.3 software (Agilent Technologies). PGCGROWTHCONDITIONS
The medium for batch culture was consisted of 11.3 g M9 medium, 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine, 10 g NaHCO3 and 9 g glucose, 50 mg ampicillin and 0.1 mmole IPTG per liter. PGCGROWTHCONDITIONS
The medium for continuous culture contained 20 g LB, 9 g glucose, 10 g NaHCO3, 50 mg ampicillin per liter and isopropyl--D-thiogalactopyranoside (IPTG) was supplemented to be 0.1 mM. The initial pH of the medium was set to be pH 7.3 by adding 1 N HCl solution. The inoculation culture was transferred into a 250 mL-fermentor containing 100 mL medium (Small scale multi-chemostat fermentor; Biotron Inc., Bucheon, Korea). The culture was performed at 37 C, 350 rpm with flushing CO2 gas at 20 mL PGCGROWTHCONDITIONS
Transcriptome of cells was prepared using a RNA extraction kit (RNeasy mini kit;Qiagen, Hilden, Germany) PGCGROWTHCONDITIONS
W3110 (KCTC 2223) PGCGROWTHCONDITIONS
W3110 overexpressing pck PGCGROWTHCONDITIONS
BnTR1, 37°C, replicate 1 PGCGROWTHCONDITIONS
BnTR1, 37°C, replicate 2 PGCGROWTHCONDITIONS
BnTR1, 37°C, replicate 3 PGCGROWTHCONDITIONS
BnTR1_37_rep1 PGCGROWTHCONDITIONS
BnTR1_37_rep2 PGCGROWTHCONDITIONS
BnTR1_37_rep3 PGCGROWTHCONDITIONS
BnTR1, 42°C, replicate 1 PGCGROWTHCONDITIONS
BnTR1, 42°C, replicate 2 PGCGROWTHCONDITIONS
BnTR1, 42°C, replicate 3 PGCGROWTHCONDITIONS
BnTR1_42_rep1 PGCGROWTHCONDITIONS
BnTR1_42_rep2 PGCGROWTHCONDITIONS
BnTR1_42_rep3 PGCGROWTHCONDITIONS
Collected cells were lysed using Trizol (Invitrogen), and total RNA was isolated using phenol-chloroform and precipitated with ice cold isopropanol. Then the precipitations were further washed with 70% ethanol and dissolved in RNase-free water. Genomic DNA was removed using RNase-free DNase I. RNA samples were further purified using RNeasy Mini Kits (Qiagen). RNA concentration and quality were determined using A Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA) and agarose gel electrophoresis. The isolated RNA was stored at −80°C before use. PGCGROWTHCONDITIONS
culture temperature: 37°C PGCGROWTHCONDITIONS
culture temperature: 42°C PGCGROWTHCONDITIONS
E. coli cells with or without BnTR1 were transferred and incubated at 37°C and 42°C for 1 hour, respectively PGCGROWTHCONDITIONS
E. coli Rosetta cells transformed with pET-28a or pET-28a-BnTR1 (OD600nm = 0.6) were induced with 0.1 mM IPTG at 37°C for 1 hour. PGCGROWTHCONDITIONS
Emplty Vector, 37°C, replicate 1 PGCGROWTHCONDITIONS
Emplty Vector, 37°C, replicate 2 PGCGROWTHCONDITIONS
Emplty Vector, 37°C, replicate 3 PGCGROWTHCONDITIONS
Emplty Vector, 42°C, replicate 1 PGCGROWTHCONDITIONS
Emplty Vector, 42°C, replicate 2 PGCGROWTHCONDITIONS
Emplty Vector, 42°C, replicate 3 PGCGROWTHCONDITIONS
EmptyVector_37_rep1 PGCGROWTHCONDITIONS
EmptyVector_37_rep2 PGCGROWTHCONDITIONS
EmptyVector_37_rep3 PGCGROWTHCONDITIONS
EmptyVector_42_rep1 PGCGROWTHCONDITIONS
EmptyVector_42_rep2 PGCGROWTHCONDITIONS
EmptyVector_42_rep3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Raw data were normalized (quantile method), merged and filtered by Feature Extraction Software (Agilent Technologies Inc.). For the sibiling probes (multiple probes to one gene), we used the median indensity for representation. PGCGROWTHCONDITIONS
vector: pET-28a PGCGROWTHCONDITIONS
vector: pET-28a-BnTR1 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w PGCGROWTHCONDITIONS
∆dapF parent Sample 28 PGCGROWTHCONDITIONS
∆dapF parent Sample 47 PGCGROWTHCONDITIONS
∆dapF parent Sample 9 PGCGROWTHCONDITIONS
dapF suppressor 1-1 Sample 10 PGCGROWTHCONDITIONS
dapF suppressor 1-1 Sample 29 PGCGROWTHCONDITIONS
dapF suppressor 1-1 Sample 48 PGCGROWTHCONDITIONS
dapF suppressor 3-1 Sample 11 PGCGROWTHCONDITIONS
dapF suppressor 3-1 Sample 30 PGCGROWTHCONDITIONS
dapF suppressor 3-1 Sample 49 PGCGROWTHCONDITIONS
∆dgk parent Sample 16 PGCGROWTHCONDITIONS
∆dgk parent Sample 35 PGCGROWTHCONDITIONS
∆dgk parent Sample 54 PGCGROWTHCONDITIONS
dgk suppressor 1-1 Sample 17 PGCGROWTHCONDITIONS
dgk suppressor 1-1 Sample 36 PGCGROWTHCONDITIONS
dgk suppressor 1-1 Sample 55 PGCGROWTHCONDITIONS
dgk suppressor 2-1 Sample 18 PGCGROWTHCONDITIONS
dgk suppressor 2-1 Sample 37 PGCGROWTHCONDITIONS
dgk suppressor 2-1 Sample 56 PGCGROWTHCONDITIONS
dgk suppressor 3-1 Sample 19 PGCGROWTHCONDITIONS
dgk suppressor 3-1 Sample 38 PGCGROWTHCONDITIONS
dgk suppressor 3-1 Sample 57 PGCGROWTHCONDITIONS
∆entC parent Sample 12 PGCGROWTHCONDITIONS
∆entC parent Sample 31 PGCGROWTHCONDITIONS
∆entC parent Sample 50 PGCGROWTHCONDITIONS
entC suppressor 1-1 Sample 13 PGCGROWTHCONDITIONS
entC suppressor 1-1 Sample 32 PGCGROWTHCONDITIONS
entC suppressor 1-1 Sample 51 PGCGROWTHCONDITIONS
entC suppressor 2-1 Sample 14 PGCGROWTHCONDITIONS
entC suppressor 2-1 Sample 33 PGCGROWTHCONDITIONS
entC suppressor 2-1 Sample 52 PGCGROWTHCONDITIONS
entC suppressor 3-1 Sample 15 PGCGROWTHCONDITIONS
entC suppressor 3-1 Sample 34 PGCGROWTHCONDITIONS
entC suppressor 3-1 Sample 53 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
∆ppk parent Sample 24 PGCGROWTHCONDITIONS
∆ppk parent Sample 43 PGCGROWTHCONDITIONS
∆ppk parent Sample 5 PGCGROWTHCONDITIONS
ppk suppressor 1-1 Sample 25 PGCGROWTHCONDITIONS
ppk suppressor 1-1 Sample 44 PGCGROWTHCONDITIONS
ppk suppressor 1-1 Sample 6 PGCGROWTHCONDITIONS
ppk suppressor 2-1 Sample 26 PGCGROWTHCONDITIONS
ppk suppressor 2-1 Sample 45 PGCGROWTHCONDITIONS
ppk suppressor 2-1 Sample 7 PGCGROWTHCONDITIONS
ppk suppressor 3-1 Sample 27 PGCGROWTHCONDITIONS
ppk suppressor 3-1 Sample 46 PGCGROWTHCONDITIONS
ppk suppressor 3-1 Sample 8 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
WT- Keio Sample 1 PGCGROWTHCONDITIONS
WT- Keio Sample 20 PGCGROWTHCONDITIONS
WT- Keio Sample 39 PGCGROWTHCONDITIONS
∆zwf parent Sample 2 PGCGROWTHCONDITIONS
∆zwf parent Sample 21 PGCGROWTHCONDITIONS
∆zwf parent Sample 40 PGCGROWTHCONDITIONS
zwf suppressor 1-1 Sample 22 PGCGROWTHCONDITIONS
zwf suppressor 1-1 Sample 3 PGCGROWTHCONDITIONS
zwf suppressor 1-1 Sample 41 PGCGROWTHCONDITIONS
zwf suppressor 1-2 Sample 23 PGCGROWTHCONDITIONS
zwf suppressor 1-2 Sample 4 PGCGROWTHCONDITIONS
zwf suppressor 1-2 Sample 42 PGCGROWTHCONDITIONS
conducted by CeGaT (Tübingen, Germany) according to SOLiD standard protocols for RNA-seq PGCGROWTHCONDITIONS
conversion: Convert SOLiD output to fastq (Galaxy Version 1.0.0); default parameters. PGCGROWTHCONDITIONS
counting: countOverlaps of Iranges; default parameters PGCGROWTHCONDITIONS
culture: 18 h at 37°C PGCGROWTHCONDITIONS
differential expression: Bioconductor package edgeR (version 3.2.3); default parameters PGCGROWTHCONDITIONS
EHEC PGCGROWTHCONDITIONS
EHEC either grown on plain LB plates or LB plates containing Symbioflor within the agar PGCGROWTHCONDITIONS
EHEC plus Symbioflor PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655 PGCGROWTHCONDITIONS
LB agar plates, 37°C for 18 h PGCGROWTHCONDITIONS
mapping: bowtie (Galaxy Version 1.1.2); 28 nt seed length, maximal two mismatches in the seed, a maximal threshold of 70 for the sum of the quality values at mismatched positions. PGCGROWTHCONDITIONS
medium: LB PGCGROWTHCONDITIONS
normalizing: convert counts in RPKM using Excel PGCGROWTHCONDITIONS
plus Symbioflor PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
scraping bacteria, opening with bead beating, Trizol-based RNA isolation, rRNA depletion with RiboZero, DNA digest, SoLiD seq by CeGaT (Tübingen, Germany) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx: logFC and p-value PGCGROWTHCONDITIONS
symbioflor status: without Symbioflor PGCGROWTHCONDITIONS
symbioflor status: with Symbioflor PGCGROWTHCONDITIONS
without Symbioflor PGCGROWTHCONDITIONS
Co-hybridization of E. coli G 1 PGCGROWTHCONDITIONS
Co-hybridization of E. coli G 3 PGCGROWTHCONDITIONS
Co-hybridization of E. coli G 4 PGCGROWTHCONDITIONS
Co-hybridization of E. coli G5 isolate with E. coli K-12 MG1655 PGCGROWTHCONDITIONS
Co-hybridization of E. coli G5 isolate with E. coli O157:H7 EDL933 PGCGROWTHCONDITIONS
Co-hybridization of E. coli isolate G 3 PGCGROWTHCONDITIONS
Co-hybridization of E. coli isolate G 4 PGCGROWTHCONDITIONS
Co-hybridization of E. coli O157:H7 EDL933 with E. coli K-12 M1655 #1 PGCGROWTHCONDITIONS
Co-hybridization of E. coli O157:H7 EDL933 with E. coli K-12 M1655 #2 PGCGROWTHCONDITIONS
control strain K-12 MG1655 PGCGROWTHCONDITIONS
control strain O157:H7 EDL933 PGCGROWTHCONDITIONS
E. coli G 1 PGCGROWTHCONDITIONS
E. coli G4 PGCGROWTHCONDITIONS
E. coli G5 PGCGROWTHCONDITIONS
E. coli isolate G 1 PGCGROWTHCONDITIONS
E. coli isolate G3 PGCGROWTHCONDITIONS
E. coli isolate G 3 PGCGROWTHCONDITIONS
E. coli isolate G4 PGCGROWTHCONDITIONS
E. coli isolate G5 PGCGROWTHCONDITIONS
E. coli K-12 MG1655 PGCGROWTHCONDITIONS
E. coli O157:H7 EDL933 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA isolation according to Grimberg et al. Nucleic acids research 1989, 17(21):8893 PGCGROWTHCONDITIONS
Isolate G 1 PGCGROWTHCONDITIONS
Isolate G 3 PGCGROWTHCONDITIONS
Isolate G 4 PGCGROWTHCONDITIONS
Isolate G5 of Symbioflor2 probiotic product from Symbiopharm PGCGROWTHCONDITIONS
log2 ratio of isolate PGCGROWTHCONDITIONS
overnight in Luria-Bertani (LB) broth with continuous agitation PGCGROWTHCONDITIONS
overnight in Lurie-Bertani (LB) broth with continuous agitation PGCGROWTHCONDITIONS
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. PGCGROWTHCONDITIONS
Biological replicates per genotype were incubated at 1 mg PGCGROWTHCONDITIONS
E. coli ATCC 25922 marR deletion+QnrS replicate 1 PGCGROWTHCONDITIONS
E. coli ATCC 25922 marR deletion+QnrS replicate 2 PGCGROWTHCONDITIONS
E. coli ATCC 25922 QnrS replicate 1 PGCGROWTHCONDITIONS
E. coli ATCC 25922 QnrS replicate 2 PGCGROWTHCONDITIONS
E. coli ATCC 25922 Ser83Leu+QnrS replicate 1 PGCGROWTHCONDITIONS
E. coli ATCC 25922 Ser83Leu+QnrS replicate 2 PGCGROWTHCONDITIONS
E. coli ATCC 25922 (wild-type) and EC14, EC19, EC24 (LLQR) isogenic strains were tested to evaluate the global response to relevant fix concentration of ciprofloxacin (1 mg PGCGROWTHCONDITIONS
Escherichia coli ATCC 25922 PGCGROWTHCONDITIONS
Exponential cells (DO600=0,4) PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany). PGCGROWTHCONDITIONS
substrain: ATCC 25922 PGCGROWTHCONDITIONS
substrain: EC14 PGCGROWTHCONDITIONS
substrain: EC19 PGCGROWTHCONDITIONS
substrain: EC24 PGCGROWTHCONDITIONS
Wild-type E. coli ATCC 25922 replicate 1 PGCGROWTHCONDITIONS
Wild-type E. coli ATCC 25922 replicate 2 PGCGROWTHCONDITIONS
Bacterial RNA was purified with Qiagen RNeasy mini kit, and the samples with RNA Integrity Number (RIN) >9 were used for labeling PGCGROWTHCONDITIONS
culture media: LB PGCGROWTHCONDITIONS
culture media: LB with 2.5 mM Fumaric acid PGCGROWTHCONDITIONS
EDL933_LB_I PGCGROWTHCONDITIONS
EDL933_LB_II PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
GeneSpring GX v.13.1 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
O157:H7 EDL933 in LB PGCGROWTHCONDITIONS
O157:H7 EDL933 sdhA in LB PGCGROWTHCONDITIONS
O157:H7 EDL933 sdhA in LB with FA PGCGROWTHCONDITIONS
sdhA_FA_I PGCGROWTHCONDITIONS
sdhA_FA_II PGCGROWTHCONDITIONS
sdhA_FA_III PGCGROWTHCONDITIONS
sdhA_LB_I PGCGROWTHCONDITIONS
sdhA_LB_II PGCGROWTHCONDITIONS
sdhA_LB_III PGCGROWTHCONDITIONS
strain background: EDL933 PGCGROWTHCONDITIONS
The overnight cultures of bacteria in LB broth were refreshed with the ratio of 1:100 into fresh LB broth, and incubated at 30℃ with continuous shaking until the absorbance at 590 nm reached 0.5 to 0.6. PGCGROWTHCONDITIONS
The values below 0.01 were set to 0.01. The log2 ratio of the intensity of signal channel to that of control channel was calculated and was then normalized to each slide’s median intensity ratio. The default interpretation mode was set to‘log of ratio’. Each time point was then tested separately for statistical differences using ANOVA at 5% confidence level, in conjunction with Benjamini-Hochberg multiple testing correction. PGCGROWTHCONDITIONS
with PGCGROWTHCONDITIONS
10J.0 PGCGROWTHCONDITIONS
11K.60 PGCGROWTHCONDITIONS
12L.120 PGCGROWTHCONDITIONS
200 bp insert, rRNA depletion PGCGROWTHCONDITIONS
7G.0 PGCGROWTHCONDITIONS
biological replicate: Replicate 1 PGCGROWTHCONDITIONS
biological replicate: t=0 Replicate 1 PGCGROWTHCONDITIONS
biological replicate: t=0 replicate 2 PGCGROWTHCONDITIONS
Dividing t=2 hours PGCGROWTHCONDITIONS
E. coli were sampled at times = 0, 1 hour, and 2 hours following release from stationary phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011 PGCGROWTHCONDITIONS
Growing  t=1 hour PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA sequences were quality assessed and trimmed using FastQC version 0.10.1 (www.bioinformatics.babraham.ac.uk PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH PGCGROWTHCONDITIONS
RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
Stationary phase  t=0 PGCGROWTHCONDITIONS
Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O PGCGROWTHCONDITIONS
time post release: E. coli cells 1 hour following release from Stationary phase  (t=1) PGCGROWTHCONDITIONS
time post release: E. coli cells 2 hour2 following release from Stationary phase  (t=2) PGCGROWTHCONDITIONS
time post release: E. coli cells immediately following release from Stationary phase  t=0 PGCGROWTHCONDITIONS
BW25113 hha deletion mutant LB 4hr biofilm cells PGCGROWTHCONDITIONS
BW25113 hha mutant LB glu 15 hr biofilm cells PGCGROWTHCONDITIONS
BW25113 hha mutant LB glu 24 hr biofilm cells PGCGROWTHCONDITIONS
BW25113 hha mutant LB glu 4 hr biofilm cells PGCGROWTHCONDITIONS
BW25113 w PGCGROWTHCONDITIONS
Channel 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 hha mutant after 15 hours of growth at 37C in LB glu with glasswool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 hha mutant after 24 hours of growth at 37C in LB glu with glasswool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 hha mutant after 4 hours of growth at 37C in LB glu with glasswool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 hha mutant after 4 hours of growth at 37C in LB with glasswool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 wild type after 15 hours of growth at 37C in LB glu with glasswool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 wild type after 24 hours of growth at 37C in LB glu with glasswool PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 wild type after 4 hours of growth at 37C in LB glu with glasswool. PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 wild type after 4 hours of growth at 37C in LB with glasswool. PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB glu medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB glu medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
“The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
75th percentile shift normalisation and baseline adjusted PGCGROWTHCONDITIONS
agent: 1x CORM2 PGCGROWTHCONDITIONS
agent: 1x vehicle PGCGROWTHCONDITIONS
agent: 20x CORM2 PGCGROWTHCONDITIONS
agent: 20x vehicle PGCGROWTHCONDITIONS
Cultures were maintained on tryptic soy agar (TSA) (Becton Dickinson, Le Pont Claix, France). Overnight cultures were grown in Difco Luria-Bertani (LB) broth (Lennox; Franklin Lakes, NJ, USA) at 37 °C aerobically on a shaker at 200 rpm. Bacteria (picked from 5-10 colonies) were suspended in 1 ml of PBS, yielding a suspension corresponding to the turbidity of McFarland 0.5, and diluted 1:100 in minimal salt (MS)-medium (~106 CFU PGCGROWTHCONDITIONS
E.coli-1x CORM2-rep1 PGCGROWTHCONDITIONS
E.coli-1x CORM2-rep2 PGCGROWTHCONDITIONS
E.coli-1x CORM2-rep3 PGCGROWTHCONDITIONS
E.coli-1x CORM2-rep4 PGCGROWTHCONDITIONS
E.coli-1x vehicle-rep1 PGCGROWTHCONDITIONS
E.coli-1x vehicle-rep2 PGCGROWTHCONDITIONS
E.coli-1x vehicle-rep3 PGCGROWTHCONDITIONS
E.coli-1x vehicle-rep4 PGCGROWTHCONDITIONS
E.coli-20x CORM2-rep1 PGCGROWTHCONDITIONS
E.coli-20x CORM2-rep2 PGCGROWTHCONDITIONS
E.coli-20x CORM2-rep3 PGCGROWTHCONDITIONS
E.coli-20x CORM2-rep4 PGCGROWTHCONDITIONS
E.coli-20x vehicle-rep1 PGCGROWTHCONDITIONS
E.coli-20x vehicle-rep2 PGCGROWTHCONDITIONS
E.coli-20x vehicle-rep3 PGCGROWTHCONDITIONS
E.coli-20x vehicle-rep4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Overnight cultures of ESBL7 from the original isolate, or isolates pre-exposed 20 times to CORM-2 or vehicle, were used to inoculate MS-medium, (OD620) of 0.1, followed by exposure to CORM-2 (250 µM) or vehicle for 30 min at 37 °C. PGCGROWTHCONDITIONS
RNA isolation was performed using an RNeasy mini kit (Qiagen Technologies, Hilden, Germany), according to the manufacturer’s protocol. DNA decontamination treatment was performed using Turbo DNase (Qiagen) and the quantity and purity of the purified RNA samples were determined using a spectrophotometer Nanodrop-1000 (Nanodrop Technologies Inc., Wilmington, DE, USA) by measuring the absorbance (A260, 230, 280) and calculating absorbance ratios (A260 PGCGROWTHCONDITIONS
0% rep1 PGCGROWTHCONDITIONS
0% rep2 PGCGROWTHCONDITIONS
100% rep1 PGCGROWTHCONDITIONS
100% rep2 PGCGROWTHCONDITIONS
26% rep1 PGCGROWTHCONDITIONS
26% rep2 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 0% PGCGROWTHCONDITIONS
rpos level: 100% PGCGROWTHCONDITIONS
rpos level: 26% PGCGROWTHCONDITIONS
strain: BW27786 (K-12 derivative) PGCGROWTHCONDITIONS
strain: DMS2545 (K-12 derivative) PGCGROWTHCONDITIONS
strain: DMS2564 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
7 min Nov0 ug PGCGROWTHCONDITIONS
7 min Nov500 ug PGCGROWTHCONDITIONS
80 min Nov10 ug PGCGROWTHCONDITIONS
80 min Nov5 ug PGCGROWTHCONDITIONS
A Linker-1 adapter (IDT) was ligated onto the 3' end of size selected RNA fragments, either ribosome footprints or fragmented total RNA. A cDNA library was created using Superscript III (ThermoFisher). After gel purification of the cDNA library all ssDNA fragments were circularized using CircLigase (Epicentre). For ribosome profiling samples rRNA containing circles were depleted using oligo-biotin  and streptavidin coupled Dynabeads (ThermoFisher) subtraction. A PCR amplification off the circles using HF Phusion (NEB) completed the libraries by adding Illumina Tru-Seq adapters and a unique index for each sample. PGCGROWTHCONDITIONS
All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS
Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
Reads were aligned to E.coli rRNA and tRNA using Bowtie v.0.12.0 allowing for one mismatch and reads aligning to more than one position in the genome were randomly assigned to one of those positions PGCGROWTHCONDITIONS
Remaining linker-1 reads (CTGTAGGCACCATCAAT) were removed from fastq files using fastx_clipper PGCGROWTHCONDITIONS
RF2*_exp1_mRNA PGCGROWTHCONDITIONS
RF2*_exp1_ribosome PGCGROWTHCONDITIONS
RF2*_exp3_mRNA PGCGROWTHCONDITIONS
RF2*_exp3_ribosome PGCGROWTHCONDITIONS
RF2*∆RF3_exp2_repA_mRNA PGCGROWTHCONDITIONS
RF2*∆RF3_exp2_repA_ribosome PGCGROWTHCONDITIONS
RF2*∆RF3_exp2_repB_mRNA PGCGROWTHCONDITIONS
RF2*∆RF3_exp2_repB_ribosome PGCGROWTHCONDITIONS
RF2*∆RF3_exp3_mRNA PGCGROWTHCONDITIONS
RF2*∆RF3_exp3_ribosome PGCGROWTHCONDITIONS
RF2*∆RF3_exp4_repA_mRNA PGCGROWTHCONDITIONS
RF2*∆RF3_exp4_repA_ribosome PGCGROWTHCONDITIONS
RF2*∆RF3_exp4_repB_mRNA PGCGROWTHCONDITIONS
RF2*∆RF3_exp4_repB_ribosome PGCGROWTHCONDITIONS
∆RF3_exp1_mRNA PGCGROWTHCONDITIONS
∆RF3_exp1_ribosome PGCGROWTHCONDITIONS
∆RF3_exp3_mRNA PGCGROWTHCONDITIONS
∆RF3_exp3_ribosome PGCGROWTHCONDITIONS
∆RF3_minimal_mRNA PGCGROWTHCONDITIONS
∆RF3_minimal_ribosome PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 PGCGROWTHCONDITIONS
strain: K12 MG1655 deltaprfC PGCGROWTHCONDITIONS
strain: K12 MG1655 prfB-Bstrain allele PGCGROWTHCONDITIONS
strain: K12 MG1655 prfB-Bstrain allele deltaprfC PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Bedgraph wiggle files were created for each sample and replicate for all reads aligned to the genome after computational rRNA and tRNA subtraction PGCGROWTHCONDITIONS
The aligned reads were converted to BAM files and sorted and indexed using SAMtools PGCGROWTHCONDITIONS
The remaining reads were aligned to genome using Bowtie v.0.12.0 allowing for one mismatch and reads aligning in more than one position in the genome were discarded PGCGROWTHCONDITIONS
whole cell lysate PGCGROWTHCONDITIONS
Whole cell lysates were clarified by brief centrifugation. Ribosome footprints were created using Mnase digestion (45 enzyme units per absorbance unit of lysate at 260nm). Using sucrose gradients the monosome fraction of lysate was isolated and footprints were size selected and converted to a cDNA library. Total RNA was extracted from purified lysate for a simultaneous RNA-seq library production for total RNA samples. Small RNA and ribosomal RNA subtraction was performed in total RNA samples using MEGAClear (ThermoFisher) and MicrobExpress (ThermoFisher) kits. Subtracted total RNA was then subjected to alkaline fragmentation prior to library preparation. PGCGROWTHCONDITIONS
Wiggle files were created by center mapping the reads between 20-40bps. Using a 10bp trim on either side of the read then mapping the read across the remaining location using Plastid. PGCGROWTHCONDITIONS
WT_exp1_mRNA PGCGROWTHCONDITIONS
WT_exp1_ribosome PGCGROWTHCONDITIONS
WT_exp2_mRNA PGCGROWTHCONDITIONS
WT_exp2_ribosome PGCGROWTHCONDITIONS
WT_exp3_mRNA PGCGROWTHCONDITIONS
WT_exp3_ribosome PGCGROWTHCONDITIONS
WT_exp4_mRNA PGCGROWTHCONDITIONS
WT_exp4_ribosome PGCGROWTHCONDITIONS
WT_minimal_mRNA PGCGROWTHCONDITIONS
WT_minimal_ribosome PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
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
Escherichia coli PGCGROWTHCONDITIONS
Flask state 1 (IPTG- PGCGROWTHCONDITIONS
Flask state 2 (IPTG+ PGCGROWTHCONDITIONS
Flask state 3 (IPTG- PGCGROWTHCONDITIONS
Flask state 4 (IPTG+ PGCGROWTHCONDITIONS
Flask state 5 (IPTG- PGCGROWTHCONDITIONS
Flask state 6 (IPTG+ PGCGROWTHCONDITIONS
Flask state 7 (IPTG- PGCGROWTHCONDITIONS
Flask state 8 (IPTG+ PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg PGCGROWTHCONDITIONS
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
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'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
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
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 1 (IPTG- PGCGROWTHCONDITIONS
Tube state 2 (IPTG+ PGCGROWTHCONDITIONS
Tube state 3 (IPTG- PGCGROWTHCONDITIONS
Tube state 4 (IPTG+ PGCGROWTHCONDITIONS
Tube state 5 (IPTG- PGCGROWTHCONDITIONS
Tube state 6 (IPTG+ PGCGROWTHCONDITIONS
Tube state 7 (IPTG- PGCGROWTHCONDITIONS
Tube state 8 (IPTG+ PGCGROWTHCONDITIONS
Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium. PGCGROWTHCONDITIONS
Enteroheamorragic E. coli PGCGROWTHCONDITIONS
Enteropathogenic E. coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA from O55:H6 strain ICC219 PGCGROWTHCONDITIONS
Genomic DNA from O55:H6 strain ICC221 PGCGROWTHCONDITIONS
Genomic DNA from O55:H6 strain ICC222 PGCGROWTHCONDITIONS
Genomic DNA from O55:H7 strain st58 PGCGROWTHCONDITIONS
Genomic DNA from O55:H7 strain st957 PGCGROWTHCONDITIONS
Genomic DNA from O55:H7 strain TB182A PGCGROWTHCONDITIONS
Genomic DNA from O55:H7 strain WC211 PGCGROWTHCONDITIONS
Genomic DNA from O55:H7 strain WC416 PGCGROWTHCONDITIONS
Genomic DNA was purified using the Genomic-tip 100 PGCGROWTHCONDITIONS
O157 strain Sakai PGCGROWTHCONDITIONS
O55:H6 ICC219 replicate 1 PGCGROWTHCONDITIONS
O55:H6 ICC219 replicate 2 PGCGROWTHCONDITIONS
O55:H6 ICC221 replicate 1 PGCGROWTHCONDITIONS
O55:H6 ICC221 replicate 2 PGCGROWTHCONDITIONS
O55:H6 ICC222 replicate 1 PGCGROWTHCONDITIONS
O55:H6 ICC222 replicate 2 PGCGROWTHCONDITIONS
O55:H7 st58 replicate 1 PGCGROWTHCONDITIONS
O55:H7 st58 replicate 2 PGCGROWTHCONDITIONS
O55:H7 st957 replicate 1 PGCGROWTHCONDITIONS
O55:H7 st957 replicate 2 PGCGROWTHCONDITIONS
O55:H7 TB182A replicate 1 PGCGROWTHCONDITIONS
O55:H7 TB182A replicate 2 PGCGROWTHCONDITIONS
O55:H7 WC211 replicate 1 PGCGROWTHCONDITIONS
O55:H7 WC211 replicate 2 PGCGROWTHCONDITIONS
O55:H7 WC416 replicate 1 PGCGROWTHCONDITIONS
O55:H7 WC416 replicate 2 PGCGROWTHCONDITIONS
Spots with reference signal intensities lower than the local background (LBG)  plus 5 standard deviations or with some spotting abnormalities were removed from analysis. Signal intensities of other spots were corrected by subtracting the LBG. PGCGROWTHCONDITIONS
A total of two samples were analyzed. ompR-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS
chip antibody: anti-myc (Santa Cruz Biotech, sc-28207) PGCGROWTHCONDITIONS
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37oC on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4 oC to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4oC to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65oC overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55 oC for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment. PGCGROWTHCONDITIONS
E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: ompR-8myc PGCGROWTHCONDITIONS
MACE software (https: PGCGROWTHCONDITIONS
OmpR NaCl 1 PGCGROWTHCONDITIONS
OmpR NaCl 2 PGCGROWTHCONDITIONS
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity. PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+ PGCGROWTHCONDITIONS
E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0 PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype: ompR deletion mutant PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
strain: K-12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total RNA isolated from E. coli PGCGROWTHCONDITIONS
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA). PGCGROWTHCONDITIONS
WT NaCl 1 PGCGROWTHCONDITIONS
WT NaCl 2 PGCGROWTHCONDITIONS
ΔompR NaCl 1 PGCGROWTHCONDITIONS
ΔompR NaCl 2 PGCGROWTHCONDITIONS
0min minus ciprofloxacin PGCGROWTHCONDITIONS
0min plus ciprofloxacin PGCGROWTHCONDITIONS
30min minus ciprofloxacin PGCGROWTHCONDITIONS
30min plus ciprofloxacin PGCGROWTHCONDITIONS
90min minus ciprofloxacin PGCGROWTHCONDITIONS
90min plus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, minus ciprofloxacin, 0min PGCGROWTHCONDITIONS
Clinical isolate, minus ciprofloxacin, 30min PGCGROWTHCONDITIONS
Clinical isolate, minus ciprofloxacin, 90min PGCGROWTHCONDITIONS
Clinical isolate, plus ciprofloxacin, 0min PGCGROWTHCONDITIONS
Clinical isolate, plus ciprofloxacin, 30min PGCGROWTHCONDITIONS
Clinical isolate, plus ciprofloxacin, 90min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 0min PGCGROWTHCONDITIONS
time point: 30min PGCGROWTHCONDITIONS
time point: 90min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: ciprofloxacin PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
Ancestral E. coli B REL606 strain PGCGROWTHCONDITIONS
A pool of 3 E. coli clones forming large colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium. PGCGROWTHCONDITIONS
A pool of 3 E. coli clones forming small colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium. PGCGROWTHCONDITIONS
A pool of 3 E. coli clones forming small colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium.  PGCGROWTHCONDITIONS
A, TP1 PGCGROWTHCONDITIONS
A, TP2 PGCGROWTHCONDITIONS
A, TP3 PGCGROWTHCONDITIONS
A, TP4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 12 hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 12hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18 hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 3.5 hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 4 hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 4hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 7hours 37°C, 250rpm. Extraction was performed just after. PGCGROWTHCONDITIONS
LA_TP1_repl1 PGCGROWTHCONDITIONS
LA_TP1_repl2 PGCGROWTHCONDITIONS
LA_TP1_repl3 PGCGROWTHCONDITIONS
LA_TP1_repl4 PGCGROWTHCONDITIONS
LA_TP1_repl5 PGCGROWTHCONDITIONS
LA_TP2_repl1 PGCGROWTHCONDITIONS
LA_TP2_repl2 PGCGROWTHCONDITIONS
LA_TP2_repl3 PGCGROWTHCONDITIONS
LA_TP2_repl4 PGCGROWTHCONDITIONS
LA_TP2_repl5 PGCGROWTHCONDITIONS
LA_TP3_repl1 PGCGROWTHCONDITIONS
LA_TP3_repl2 PGCGROWTHCONDITIONS
LA_TP3_repl3 PGCGROWTHCONDITIONS
LA_TP3_repl4 PGCGROWTHCONDITIONS
LA_TP3_repl5 PGCGROWTHCONDITIONS
LA_TP4_repl1 PGCGROWTHCONDITIONS
LA_TP4_repl2 PGCGROWTHCONDITIONS
LA_TP4_repl3 PGCGROWTHCONDITIONS
LA_TP4_repl4 PGCGROWTHCONDITIONS
LA_TP4_repl5 PGCGROWTHCONDITIONS
L, TP1 PGCGROWTHCONDITIONS
L, TP2 PGCGROWTHCONDITIONS
L, TP3 PGCGROWTHCONDITIONS
L, TP4 PGCGROWTHCONDITIONS
SA_TP1_repl1 PGCGROWTHCONDITIONS
SA_TP1_repl2 PGCGROWTHCONDITIONS
SA_TP1_repl3 PGCGROWTHCONDITIONS
SA_TP1_repl4 PGCGROWTHCONDITIONS
SA_TP1_repl5 PGCGROWTHCONDITIONS
SA_TP2_repl1 PGCGROWTHCONDITIONS
SA_TP2_repl2 PGCGROWTHCONDITIONS
SA_TP2_repl3 PGCGROWTHCONDITIONS
SA_TP2_repl4 PGCGROWTHCONDITIONS
SA_TP2_repl5 PGCGROWTHCONDITIONS
SA_TP3_repl1 PGCGROWTHCONDITIONS
SA_TP3_repl2 PGCGROWTHCONDITIONS
SA_TP3_repl3 PGCGROWTHCONDITIONS
SA_TP3_repl4 PGCGROWTHCONDITIONS
SA_TP3_repl5 PGCGROWTHCONDITIONS
SA_TP4_repl1 PGCGROWTHCONDITIONS
SA_TP4_repl2 PGCGROWTHCONDITIONS
SA_TP4_repl3 PGCGROWTHCONDITIONS
SA_TP4_repl4 PGCGROWTHCONDITIONS
SA_TP4_repl5 PGCGROWTHCONDITIONS
Statistical preprocessing steps were conducted with ArrayPipe (version 1.7), a web-based software designed for processing of microarray data (www.pathogenomics.ca PGCGROWTHCONDITIONS
S, TP1 PGCGROWTHCONDITIONS
S, TP2 PGCGROWTHCONDITIONS
S, TP3 PGCGROWTHCONDITIONS
S, TP4 PGCGROWTHCONDITIONS
Total RNA was extracted using Qiagen RNeasy Mini Kit. DNA was removed using Ambion DNA-free kit. RNA quality was assessed using 2% agarose gels and OD260 PGCGROWTHCONDITIONS
VALUEs are calculated as log2-transformed (test PGCGROWTHCONDITIONS
dnaC2 30' at 30 deg, 2 ug gen DNA, pdN6 RT PGCGROWTHCONDITIONS
dnaC2 90' at 42 deg, 2 ug gen DNA, pdN6 RT PGCGROWTHCONDITIONS
dnaC2 synchrony 30' after shift, print 7 array PGCGROWTHCONDITIONS
dnaC fully replicated, 2 ug Sau3AI, pdN6 RT PGCGROWTHCONDITIONS
dnaC fully replicated, 2 ug Say3AI, pdN6 RT PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Basecalls performed using Illumina CASAVA. PGCGROWTHCONDITIONS
Cells were induced with arabinose or heat shocked, then harvested and flash frozen. PGCGROWTHCONDITIONS
Cells were lysed in liquid nitrogen, then samples were taken for ribosome footprint extraction. PGCGROWTHCONDITIONS
Cells were lysed in liquid nitrogen, then samples were taken for total RNA. PGCGROWTHCONDITIONS
E. coli cultures PGCGROWTHCONDITIONS
ecoli_k12_30C_f_1 PGCGROWTHCONDITIONS
ecoli_k12_30C_f_2 PGCGROWTHCONDITIONS
ecoli_k12_30C_f_3 PGCGROWTHCONDITIONS
ecoli_k12_30C_m_1 PGCGROWTHCONDITIONS
ecoli_k12_30C_m_2 PGCGROWTHCONDITIONS
ecoli_k12_30C_m_3 PGCGROWTHCONDITIONS
ecoli_k12_42C_10min_f_1 PGCGROWTHCONDITIONS
ecoli_k12_42C_10min_f_2 PGCGROWTHCONDITIONS
ecoli_k12_42C_10min_f_3 PGCGROWTHCONDITIONS
ecoli_k12_42C_10min_m_1 PGCGROWTHCONDITIONS
ecoli_k12_42C_10min_m_2 PGCGROWTHCONDITIONS
ecoli_k12_42C_10min_m_3 PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_f_1 PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_f_2 PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_f_3 PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_m_1 PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_m_2 PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_m_3 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_f_1 PGCGROWTHCONDITIONS
ecoli_k12_pBad_30C_f_2 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_f_3 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_f_4 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_m_1 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_m_2 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_m_3 PGCGROWTHCONDITIONS
ecoli_k12_pBAD_30C_m_4 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32I54N_30C_f_1 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32I54N_30C_f_2 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32I54N_30C_m_1 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32I54N_30C_m_2 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32wt_30C_f_1 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32wt_30C_f_2 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32wt_30C_f_3 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32wt_30C_m_1 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32wt_30C_m_2 PGCGROWTHCONDITIONS
ecoli_k12_pBADsigma32wt_30C_m_3 PGCGROWTHCONDITIONS
E. coli were grown in defined rich media at 30C. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
growth temperature: 30C PGCGROWTHCONDITIONS
heat shock time: 0min PGCGROWTHCONDITIONS
heat shock time: 10min PGCGROWTHCONDITIONS
heat shock time: 20min PGCGROWTHCONDITIONS
heat shock time: None PGCGROWTHCONDITIONS
induction: 0.2% arabinose PGCGROWTHCONDITIONS
induction: None PGCGROWTHCONDITIONS
Library strategy: Ribo-Seq PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
plasmid: None PGCGROWTHCONDITIONS
plasmid: pBAD PGCGROWTHCONDITIONS
plasmid: pBADsigma32I54N PGCGROWTHCONDITIONS
plasmid: pBADsigma32wt PGCGROWTHCONDITIONS
Polysomes were digested with MNase, monosomes were purified by sucrose gradient ultracentrifugation, and the resulting mRNA fragments were extracted with phenol chloroform and gel-purified. PGCGROWTHCONDITIONS
Reads were aligned to the MG1655 genome with Bowtie. PGCGROWTHCONDITIONS
Reads were trimmed and adaptors removed using the fastx_toolkit. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
replicate: 4 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was dephosphorylated, ligated to an adaptor, reverse transcribed, circularized then amplified with Illumina adaptors and barcodes. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: ecoli_heatshock_normalizedcounts.txt: Tab-delimited text file has EdgeR-normalized counts per kilobase million for each E. coli gene (EcoCyc gene names). PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: ecoli_heatshock_rawcounts.txt: Tab-delimited text file has raw read counts per kilobase million for each E. coli gene (EcoCyc gene names). PGCGROWTHCONDITIONS
The number of reads at each position in the genome was counted using in-house Python scripts. PGCGROWTHCONDITIONS
The number of reads mapping to each gene was counted and normalized using EdgeR. PGCGROWTHCONDITIONS
Total RNA was extracted with phenol chloroform and alkaline fragmented, then fragments (20-40 nt) were gel-purified. PGCGROWTHCONDITIONS
treatment temperature: 30C PGCGROWTHCONDITIONS
treatment temperature: 42C PGCGROWTHCONDITIONS
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome. PGCGROWTHCONDITIONS
Blue_1 PGCGROWTHCONDITIONS
Blue_2 PGCGROWTHCONDITIONS
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius PGCGROWTHCONDITIONS
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one pale colony and grown for 5 hr at 37 degrees celsius PGCGROWTHCONDITIONS
Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius.  Cells were pelleted by centrifugation and flash frozen on dry ice. PGCGROWTHCONDITIONS
Pale_1 PGCGROWTHCONDITIONS
Pale_3 PGCGROWTHCONDITIONS
parent strain: BW27785 PGCGROWTHCONDITIONS
phenotype: Blue colony-color (prion-containing) PGCGROWTHCONDITIONS
phenotype: Pale colony-color (prion-lacking) PGCGROWTHCONDITIONS
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina).  cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Specifically, data were treated as two experiments constituting either two (lue\ cell transcriptomes) or three (\pale\ cell transcriptomes) biological replicates. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two (lue\ cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three (\pale\ cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates.  Gene annotation, gene product description, and strand information is also included. PGCGROWTHCONDITIONS
Total RNA extracted from Rho prion-containing cells PGCGROWTHCONDITIONS
Total RNA extracted from Rho prion-lacking cells PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets with TRI Reagent (MRC).  RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature.  DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen). PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR  reference 1, rep1 PGCGROWTHCONDITIONS
chemostat STR culture STR reference 1 , rep2 PGCGROWTHCONDITIONS
chemostat STR culture STR  reference 2, rep1 PGCGROWTHCONDITIONS
chemostat STR culture STR reference 2 , rep2 PGCGROWTHCONDITIONS
chemostat STR culture STR  reference 3, rep1 PGCGROWTHCONDITIONS
chemostat STR culture STR reference 3 , rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 10min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 10min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 210min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 210min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 26h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 330min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 45min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 45min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 5min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 5min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 75min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 10min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 10min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 210min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 210min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 26h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 26h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 330min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 330min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 45min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 45min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 5min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 5min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 75min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 75min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http: PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http: PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-15h PGCGROWTHCONDITIONS
time: 0-16h PGCGROWTHCONDITIONS
time: 0-2h PGCGROWTHCONDITIONS
time: 10min PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
time: 210min PGCGROWTHCONDITIONS
time: 25h PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
time: 26h PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
time: 330min PGCGROWTHCONDITIONS
time: 45min PGCGROWTHCONDITIONS
time: 5min PGCGROWTHCONDITIONS
time: 75min PGCGROWTHCONDITIONS
0', before UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
0' lexA, before UV 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
0' wt, before UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
ATCACG-D1 PGCGROWTHCONDITIONS
CGATGT-D2 PGCGROWTHCONDITIONS
DGE analysis used a false-discovery rate (FDR) of 0.10. PGCGROWTHCONDITIONS
Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file. PGCGROWTHCONDITIONS
Genome_build: FM180568 PGCGROWTHCONDITIONS
Genome_build: FM180569 PGCGROWTHCONDITIONS
Genome_build: FM180570 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600). PGCGROWTHCONDITIONS
Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket PGCGROWTHCONDITIONS
LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS
Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2) PGCGROWTHCONDITIONS
Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE PGCGROWTHCONDITIONS
source: Bustamante et al., 2011 PGCGROWTHCONDITIONS
strain: JPEP22 PGCGROWTHCONDITIONS
Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
TTAGGC-D3 PGCGROWTHCONDITIONS
Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL PGCGROWTHCONDITIONS
Whole bacterial cell RNA transcriptome PGCGROWTHCONDITIONS
10min after UVtreatment 1', 40J, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
10min UV treated cells, 25 ug total RNA PGCGROWTHCONDITIONS
Cells treated with bacterial protect reagent and freeze at -70 C PGCGROWTHCONDITIONS
E. coli grow in LB rich medium to OD600=2.4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genotype: E. coli K12 PGCGROWTHCONDITIONS
RNA samples were extracted via Invitrogen RNAeasy Kit and treated with DNaseI to remove all DNA PGCGROWTHCONDITIONS
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. PGCGROWTHCONDITIONS
W3110  lsrK mutants PGCGROWTHCONDITIONS
W3110 lsrK mutants PGCGROWTHCONDITIONS
W3110 lsrK mutants, biological rep1 PGCGROWTHCONDITIONS
W3110 lsrK mutants, biological rep2 PGCGROWTHCONDITIONS
W3110 lsrR  mutants PGCGROWTHCONDITIONS
W3110 lsrR mutants, biological rep1 PGCGROWTHCONDITIONS
W3110 lsrR mutants, biological rep2 PGCGROWTHCONDITIONS
W3110 wild type PGCGROWTHCONDITIONS
W3110 wild type, biological rep1 PGCGROWTHCONDITIONS
W3110 wild type, biological rep2 PGCGROWTHCONDITIONS
20min after UVtreatment 1', 40J, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
20min untreatedcells, 25 ug total RNA PGCGROWTHCONDITIONS
20min UV treated cells, 25 ug total RNA PGCGROWTHCONDITIONS
20min UVtreatment control, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
antibody: Monoclonal ANTI-FLAG M2 antibody (F3165) -Sigma PGCGROWTHCONDITIONS
background: crp mutant background, fis flag tag PGCGROWTHCONDITIONS
background: fis mutant background, crp flag tag PGCGROWTHCONDITIONS
background: wild type, crp flag tag PGCGROWTHCONDITIONS
background: wild type, fis flag tag PGCGROWTHCONDITIONS
BAM files of each ChIP biological replicate and the input replicate samples were used in the MACS peak calling program with the -f BAMPE parameter PGCGROWTHCONDITIONS
Cells were fixed in the required growth phase in formaldehyde, quenched, washed and lysed. Fragmented DNA - protein complex were pulled using the monoclonal flag tag antibody. The complex was then washed, reverse cross-linked and obtained DNA purified using Qiagen min elute PCR purification kit. PGCGROWTHCONDITIONS
Cells were inoculated from overnight culture in rich Lysogeny broth at 37 degrees in aerobic conditions. PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
crp.ee.chipseq PGCGROWTHCONDITIONS
crp.ee.input PGCGROWTHCONDITIONS
crp.me.chipseq PGCGROWTHCONDITIONS
crp.me,input PGCGROWTHCONDITIONS
crp.me.input PGCGROWTHCONDITIONS
crpmutant.fis.ee.chipseq PGCGROWTHCONDITIONS
crpmutant.fis.ee.input PGCGROWTHCONDITIONS
crpmutant.fis.me.chipseq PGCGROWTHCONDITIONS
crpmutant.fis.me.input PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
fis.ee.chipseq PGCGROWTHCONDITIONS
fis.ee.input PGCGROWTHCONDITIONS
fis.me.chipseq PGCGROWTHCONDITIONS
fis.me.input PGCGROWTHCONDITIONS
fismutant.crp.ee.chipseq PGCGROWTHCONDITIONS
fismutant.crp.ee.input PGCGROWTHCONDITIONS
fismutant.crp.me.chipseq PGCGROWTHCONDITIONS
fismutant.crp.me.input PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
SAM files thus obtained were converted to BAM files using samtools view command PGCGROWTHCONDITIONS
Samples were aligned to the E. coli K 12 MG1655 reference sequence (version NC000913.2), using BWA (version 0.5) WITH -q 30 parameter for trimming of reads below PHRED quality score of 30. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: peaks.bed PGCGROWTHCONDITIONS
Truseq ChIP kit was used for the library preparation. DNA was end repaired and adapters were ligated. After ligation, purify ligation products and then amplify. PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O PGCGROWTHCONDITIONS
E. coli MG1655  PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
ORF1_1 PGCGROWTHCONDITIONS
ORF1_1_IPTG PGCGROWTHCONDITIONS
ORF1_2 PGCGROWTHCONDITIONS
ORF1_2_IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: ORF1 replicate 1  PGCGROWTHCONDITIONS
replicates: ORF1 replicate 2  PGCGROWTHCONDITIONS
replicates: Svi3-3 replicate 1  PGCGROWTHCONDITIONS
replicates: Svi3-3 replicate 2  PGCGROWTHCONDITIONS
replicates: WT replicate 1  PGCGROWTHCONDITIONS
replicates: WT replicate 2  PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
Svi3_3_1 PGCGROWTHCONDITIONS
Svi3_3_1_IPTG PGCGROWTHCONDITIONS
Svi3_3_2 PGCGROWTHCONDITIONS
Svi3_3_2_IPTG PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
WT1_IPTG PGCGROWTHCONDITIONS
WT2_IPTG PGCGROWTHCONDITIONS
An o PGCGROWTHCONDITIONS
E. coli TolC cells were grown o PGCGROWTHCONDITIONS
Eco_TolC_0min_A PGCGROWTHCONDITIONS
Eco_TolC_0min_B PGCGROWTHCONDITIONS
Eco_TolC_15min_Carolacton_A PGCGROWTHCONDITIONS
Eco_TolC_15min_Carolacton_B PGCGROWTHCONDITIONS
Eco_TolC_15min_control_A PGCGROWTHCONDITIONS
Eco_TolC_15min_control_B PGCGROWTHCONDITIONS
Eco_TolC_30min_Carolacton_A PGCGROWTHCONDITIONS
Eco_TolC_30min_Carolacton_B PGCGROWTHCONDITIONS
Eco_TolC_30min_control_A PGCGROWTHCONDITIONS
Eco_TolC_30min_control_B PGCGROWTHCONDITIONS
Eco_TolC_5min_Carolacton_A PGCGROWTHCONDITIONS
Eco_TolC_5min_Carolacton_B PGCGROWTHCONDITIONS
Eco_TolC_5min_control_A PGCGROWTHCONDITIONS
Eco_TolC_5min_control_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https: PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 0 PGCGROWTHCONDITIONS
time point (minutes): 15 PGCGROWTHCONDITIONS
time point (minutes): 30 PGCGROWTHCONDITIONS
time point (minutes): 5 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
antibody: anti-FLAG mAb PGCGROWTHCONDITIONS
antibody vendor PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8 PGCGROWTHCONDITIONS
Cells were grown in LB media with 1mM IPTG at 37 °C with shaking for 2 hours PGCGROWTHCONDITIONS
ChIP-Seq PGCGROWTHCONDITIONS
CsiR_ChIPSeq PGCGROWTHCONDITIONS
CsiR_RNASeq PGCGROWTHCONDITIONS
Culture cells PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106). PGCGROWTHCONDITIONS
For total RNA extraction, cells were pelleted in 4 °C. PGCGROWTHCONDITIONS
Genome_build: U00096.2 (GenBank) PGCGROWTHCONDITIONS
Nac_ChIPSeq PGCGROWTHCONDITIONS
Nac_RNASeq PGCGROWTHCONDITIONS
NtrC_ChIPSeq PGCGROWTHCONDITIONS
OmpR_ChIPSeq PGCGROWTHCONDITIONS
Peak calling was done using SPAT PGCGROWTHCONDITIONS
Reads were aligned to GenBank ID U00096.2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively PGCGROWTHCONDITIONS
The appropriate protocols were performed using standard Illumina procedures PGCGROWTHCONDITIONS
Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns PGCGROWTHCONDITIONS
transcription factor: CsiR PGCGROWTHCONDITIONS
transcription factor: Nac PGCGROWTHCONDITIONS
transcription factor: NtrC PGCGROWTHCONDITIONS
transcription factor: OmpR PGCGROWTHCONDITIONS
40min after UVtreatment 1, 40J, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
40min untreatedcells, 25 ug total RNA PGCGROWTHCONDITIONS
batch: 10 PGCGROWTHCONDITIONS
batch: 11 PGCGROWTHCONDITIONS
batch: 12 PGCGROWTHCONDITIONS
batch: 13 PGCGROWTHCONDITIONS
batch: 14 PGCGROWTHCONDITIONS
batch: 15 PGCGROWTHCONDITIONS
batch: 16 PGCGROWTHCONDITIONS
batch: 17 PGCGROWTHCONDITIONS
batch: 18 PGCGROWTHCONDITIONS
batch: 19 PGCGROWTHCONDITIONS
batch: 20 PGCGROWTHCONDITIONS
batch: 21 PGCGROWTHCONDITIONS
batch: 22 PGCGROWTHCONDITIONS
batch: 23 PGCGROWTHCONDITIONS
batch: 24 PGCGROWTHCONDITIONS
batch: 25 PGCGROWTHCONDITIONS
batch: 26 PGCGROWTHCONDITIONS
batch: 27 PGCGROWTHCONDITIONS
batch: 7 PGCGROWTHCONDITIONS
batch: 8 PGCGROWTHCONDITIONS
batch: 9 PGCGROWTHCONDITIONS
bowtie2-build final_reference_seqs PGCGROWTHCONDITIONS
carbon source: gluconate PGCGROWTHCONDITIONS
carbon source: glucose PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
carbon source: lactate PGCGROWTHCONDITIONS
convert back to sorted.sam with samtools PGCGROWTHCONDITIONS
convert bowtie output .sam to .bam with samtools PGCGROWTHCONDITIONS
Escherichia coli B str. REL606 PGCGROWTHCONDITIONS
exponential culture PGCGROWTHCONDITIONS
Genome_build: reference sequence is REL606 PGCGROWTHCONDITIONS
get raw counts for reads mapped with htseq-count PGCGROWTHCONDITIONS
gluconate_growth: MURI_091 PGCGROWTHCONDITIONS
gluconate_growth: MURI_092 PGCGROWTHCONDITIONS
gluconate_growth: MURI_093 PGCGROWTHCONDITIONS
gluconate_growth: MURI_094 PGCGROWTHCONDITIONS
gluconate_growth: MURI_095 PGCGROWTHCONDITIONS
gluconate_growth: MURI_096 PGCGROWTHCONDITIONS
glucose_time_course: MURI_016 PGCGROWTHCONDITIONS
glucose_time_course: MURI_017 PGCGROWTHCONDITIONS
glucose_time_course: MURI_018 PGCGROWTHCONDITIONS
glucose_time_course: MURI_019 PGCGROWTHCONDITIONS
glucose_time_course: MURI_020 PGCGROWTHCONDITIONS
glucose_time_course: MURI_021 PGCGROWTHCONDITIONS
glucose_time_course: MURI_022 PGCGROWTHCONDITIONS
glucose_time_course: MURI_023 PGCGROWTHCONDITIONS
glucose_time_course: MURI_024 PGCGROWTHCONDITIONS
glucose_time_course: MURI_025 PGCGROWTHCONDITIONS
glucose_time_course: MURI_026 PGCGROWTHCONDITIONS
glucose_time_course: MURI_027 PGCGROWTHCONDITIONS
glucose_time_course: MURI_028 PGCGROWTHCONDITIONS
glucose_time_course: MURI_029 PGCGROWTHCONDITIONS
glucose_time_course: MURI_030 PGCGROWTHCONDITIONS
glucose_time_course: MURI_031 PGCGROWTHCONDITIONS
glucose_time_course: MURI_032 PGCGROWTHCONDITIONS
glucose_time_course: MURI_033 PGCGROWTHCONDITIONS
glucose_time_course: MURI_097 PGCGROWTHCONDITIONS
glucose_time_course: MURI_098 PGCGROWTHCONDITIONS
glucose_time_course: MURI_099 PGCGROWTHCONDITIONS
glucose_time_course: MURI_100 PGCGROWTHCONDITIONS
glucose_time_course: MURI_101 PGCGROWTHCONDITIONS
glucose_time_course: MURI_102 PGCGROWTHCONDITIONS
glucose_time_course: MURI_103 PGCGROWTHCONDITIONS
glucose_time_course: MURI_104 PGCGROWTHCONDITIONS
glucose_time_course: MURI_105 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_034 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_035 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_036 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_037 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_038 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_039 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_040 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_041 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_042 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_043 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_044 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_045 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_046 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_047 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_048 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_049 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_050 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_052 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_053 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_054 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_055 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_056 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_057 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_058 PGCGROWTHCONDITIONS
glycerol_time_course: MURI_059 PGCGROWTHCONDITIONS
growth phase: exponential PGCGROWTHCONDITIONS
growth phase: late_stationary PGCGROWTHCONDITIONS
growth phase: stationary PGCGROWTHCONDITIONS
growth time (hours): 10 PGCGROWTHCONDITIONS
growth time (hours): 14 PGCGROWTHCONDITIONS
growth time (hours): 168 PGCGROWTHCONDITIONS
growth time (hours): 24 PGCGROWTHCONDITIONS
growth time (hours): 26 PGCGROWTHCONDITIONS
growth time (hours): 27 PGCGROWTHCONDITIONS
growth time (hours): 28 PGCGROWTHCONDITIONS
growth time (hours): 29 PGCGROWTHCONDITIONS
growth time (hours): 3 PGCGROWTHCONDITIONS
growth time (hours): 336 PGCGROWTHCONDITIONS
growth time (hours): 4 PGCGROWTHCONDITIONS
growth time (hours): 48 PGCGROWTHCONDITIONS
growth time (hours): 5 PGCGROWTHCONDITIONS
growth time (hours): 5.5 PGCGROWTHCONDITIONS
growth time (hours): 6 PGCGROWTHCONDITIONS
growth time (hours): 6.5 PGCGROWTHCONDITIONS
growth time (hours): 7 PGCGROWTHCONDITIONS
growth time (hours): 8 PGCGROWTHCONDITIONS
growth time (hours): 9 PGCGROWTHCONDITIONS
Illumina Ribozero rRNA removal followed by NEB Next RNA library Prep set. PGCGROWTHCONDITIONS
lactate_growth: MURI_085 PGCGROWTHCONDITIONS
lactate_growth: MURI_086 PGCGROWTHCONDITIONS
lactate_growth: MURI_087 PGCGROWTHCONDITIONS
lactate_growth: MURI_088 PGCGROWTHCONDITIONS
lactate_growth: MURI_089 PGCGROWTHCONDITIONS
lactate_growth: MURI_090 PGCGROWTHCONDITIONS
late stationary culture PGCGROWTHCONDITIONS
map trimmed reads to reference sequence in indexes file with bowtie2 PGCGROWTHCONDITIONS
mg+2 (levels): baseMg PGCGROWTHCONDITIONS
mg+2 (levels): highMg PGCGROWTHCONDITIONS
mg+2 (levels): lowMg PGCGROWTHCONDITIONS
mg+2 (mm): 0.005 PGCGROWTHCONDITIONS
mg+2 (mm): 0.01 PGCGROWTHCONDITIONS
mg+2 (mm): 0.02 PGCGROWTHCONDITIONS
mg+2 (mm): 0.04 PGCGROWTHCONDITIONS
mg+2 (mm): 0.08 PGCGROWTHCONDITIONS
mg+2 (mm): 0.8 PGCGROWTHCONDITIONS
mg+2 (mm): 200 PGCGROWTHCONDITIONS
mg+2 (mm): 400 PGCGROWTHCONDITIONS
mg+2 (mm): 50 PGCGROWTHCONDITIONS
mg+2 (mm): 8 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_106 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_107 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_108 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_109 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_110 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_111 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_112 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_113 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_114 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_115 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_116 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_117 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_118 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_119 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_120 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_121 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_122 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_123 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_124 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_125 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_126 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_127 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_128 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_129 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_130 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_131 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_132 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_133 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_134 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_135 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_136 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_137 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_138 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_139 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_140 PGCGROWTHCONDITIONS
MgSO4_stress_high: MURI_141 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_142 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_143 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_144 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_145 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_146 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_147 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_148 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_149 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_150 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_151 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_152 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_153 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_154 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_155 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_156 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_157 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_158 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_159 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_160 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_161 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_162 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_163 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_164 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_165 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_166 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_167 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_168 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_169 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_170 PGCGROWTHCONDITIONS
MgSO4_stress_low: MURI_171 PGCGROWTHCONDITIONS
na+1 (levels): baseNa PGCGROWTHCONDITIONS
na+1 (levels): highNa PGCGROWTHCONDITIONS
na+1 (mm): 100 PGCGROWTHCONDITIONS
na+1 (mm): 200 PGCGROWTHCONDITIONS
na+1 (mm): 300 PGCGROWTHCONDITIONS
na+1 (mm): 5 PGCGROWTHCONDITIONS
NaCl_stress: MURI_061 PGCGROWTHCONDITIONS
NaCl_stress: MURI_063 PGCGROWTHCONDITIONS
NaCl_stress: MURI_064 PGCGROWTHCONDITIONS
NaCl_stress: MURI_065 PGCGROWTHCONDITIONS
NaCl_stress: MURI_066 PGCGROWTHCONDITIONS
NaCl_stress: MURI_067 PGCGROWTHCONDITIONS
NaCl_stress: MURI_068 PGCGROWTHCONDITIONS
NaCl_stress: MURI_069 PGCGROWTHCONDITIONS
NaCl_stress: MURI_070 PGCGROWTHCONDITIONS
NaCl_stress: MURI_071 PGCGROWTHCONDITIONS
NaCl_stress: MURI_072 PGCGROWTHCONDITIONS
NaCl_stress: MURI_073 PGCGROWTHCONDITIONS
NaCl_stress: MURI_074 PGCGROWTHCONDITIONS
NaCl_stress: MURI_075 PGCGROWTHCONDITIONS
NaCl_stress: MURI_076 PGCGROWTHCONDITIONS
NaCl_stress: MURI_077 PGCGROWTHCONDITIONS
NaCl_stress: MURI_079 PGCGROWTHCONDITIONS
NaCl_stress: MURI_080 PGCGROWTHCONDITIONS
NaCl_stress: MURI_081 PGCGROWTHCONDITIONS
NaCl_stress: MURI_082 PGCGROWTHCONDITIONS
NaCl_stress: MURI_083 PGCGROWTHCONDITIONS
NaCl_stress: MURI_084 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap followed by purification through Zymo RNA clean and concentrator. PGCGROWTHCONDITIONS
stationary culture PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt files including count numbers of RNA's and quality control were generated PGCGROWTHCONDITIONS
trim adaptors on raw reads and moved trimmed reads to trimmed_reads with flexbar PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
Data were normalized using the LOWESS algorithm and analyzed for statistical significance using the MeV package PGCGROWTHCONDITIONS
EJW3, BW25113 rpoC K370_A396dup PGCGROWTHCONDITIONS
EJW3 in M9 Replicate 1 PGCGROWTHCONDITIONS
EJW3 in M9 Replicate 2 PGCGROWTHCONDITIONS
EJW3 in M9 supplemented with 0.6 M NaCl Replicate 1 PGCGROWTHCONDITIONS
EJW3 in M9 supplemented with 0.6 M NaCl Replicate 2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
EYG1 in M9 Replicate 1 PGCGROWTHCONDITIONS
EYG1 in M9 Replicate 2 PGCGROWTHCONDITIONS
EYG1, MG1655 rpoC K370_A396dup PGCGROWTHCONDITIONS
EYG in M9 supplemented with 0.6 M NaCl Replicate 1 PGCGROWTHCONDITIONS
EYG in M9 supplemented with 0.6 M NaCl Replicate 2 PGCGROWTHCONDITIONS
genotype: rpoC K370_A396dup mutant PGCGROWTHCONDITIONS
genotype: Wild-type strain PGCGROWTHCONDITIONS
Grown in glucose M9 media with or without supplementation of 0.6 M NaCl PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
protocol: M9 PGCGROWTHCONDITIONS
protocol: M9 supplemented with 0.6 M NaCl PGCGROWTHCONDITIONS
Samples were grown to mid exponential phase (OD approx 0.5). Cultures were then quickly chilled to ≤ 4 ºC on dry ice PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
control strain PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
L-threonine producing strain PGCGROWTHCONDITIONS
L-threonine producing strain vs control strain PGCGROWTHCONDITIONS
The mean signal intensity values of the duplicate spots were averaged and then normalized by the global normalization method. The genes showing the p-values lower than 0.05 were considered to be significant. PGCGROWTHCONDITIONS
using RNeasy Mini Kit PGCGROWTHCONDITIONS
W3110 (lacI-deleted) strain harboring pKK223-3 PGCGROWTHCONDITIONS
ATCC2 PGCGROWTHCONDITIONS
ATCC3 PGCGROWTHCONDITIONS
Broiler Fecal PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing PGCGROWTHCONDITIONS
Following \TruSeq RNA Sample Preparation Guide\. PGCGROWTHCONDITIONS
Genome_build: UCSC mm10 PGCGROWTHCONDITIONS
Human PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8 PGCGROWTHCONDITIONS
strain: E. coli ATCC 25922 PGCGROWTHCONDITIONS
strain: Poultry E. coli Virulent and multidrug resistant PGCGROWTHCONDITIONS
Strains were harvested in MH broth at log phase PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample PGCGROWTHCONDITIONS
Total RNAs were extracted from the bacterial isolates using TRIzol PGCGROWTHCONDITIONS
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform PGCGROWTHCONDITIONS
biomass collected in the transition between exponential to stationary phase PGCGROWTHCONDITIONS
EHEC in LB Experiment 1 [RIBO-Seq] PGCGROWTHCONDITIONS
EHEC in LB Experiment 1 [RNA-Seq] PGCGROWTHCONDITIONS
EHEC in LB Experiment 2 [RIBO-Seq] PGCGROWTHCONDITIONS
EHEC in LB Experiment 2 [RNA-Seq] PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655 PGCGROWTHCONDITIONS
growth media: LB medium PGCGROWTHCONDITIONS
Illumina fastq files were submitted to the galaxy pipeline => grooming => mapping to NC_002655 using bowtie2 (default but seed 19 nt & zero mismatches within seed) PGCGROWTHCONDITIONS
LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase PGCGROWTHCONDITIONS
Library strategy: RIBO-seq PGCGROWTHCONDITIONS
ligation, rt-PCR, PCR PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Reads, RPKM, and RCV mapped to NC_002655 (RCV = Ribosomal Coverage Value = RPKM-footprint over RPKM-transcription) PGCGROWTHCONDITIONS
Trizol for RNAseq, gradient centrifugation => RNase digestions => Trizol => gel extraction for RIBOseq PGCGROWTHCONDITIONS
Truseq Small RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_018220 and NC_000913 PGCGROWTHCONDITIONS
MG1655_LB PGCGROWTHCONDITIONS
MG1655_LB1 PGCGROWTHCONDITIONS
MG1655_LB2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition PGCGROWTHCONDITIONS
We use Rockhopper for alignment and the complete analysis of data PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time0 PGCGROWTHCONDITIONS
rnc-_time10 PGCGROWTHCONDITIONS
rnc-_time20 PGCGROWTHCONDITIONS
rnc-_time2.5 PGCGROWTHCONDITIONS
rnc-_time5 PGCGROWTHCONDITIONS
rnc-_time7.5 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time0 PGCGROWTHCONDITIONS
time point: time10 PGCGROWTHCONDITIONS
time point: time20 PGCGROWTHCONDITIONS
time point: time2.5 PGCGROWTHCONDITIONS
time point: time5 PGCGROWTHCONDITIONS
time point: time7.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time0 PGCGROWTHCONDITIONS
WTA_time10 PGCGROWTHCONDITIONS
WTA_time20 PGCGROWTHCONDITIONS
WTA_time2.5 PGCGROWTHCONDITIONS
WTA_time5 PGCGROWTHCONDITIONS
WTA_time7.5 PGCGROWTHCONDITIONS
WTB_time0 PGCGROWTHCONDITIONS
WTB_time2.5 PGCGROWTHCONDITIONS
WTB_time7.5 PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent (or mature) RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant (Epicentre, cat. LR2D11310K) in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 20 μl of Fragmentation buffer [65 mM Tris pH 8.3; 100 mM KCl; 5 mM MgCl2]. RNA was fragmented by incubation at 95°C for 8 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns, and eluted in 5.5 μl of nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, cat. 10777-019), and 100 U SuperScript® III Reverse Transcriptase (Invitrogen, cat. 18080-044), by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range 40-150 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent RNA (either total, or rRNA-depleted using Ribo-Zero rRNA Removal Kit (Illumina, cat. MRZB12424)) in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 5.5 μl nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, and 100 U SuperScript® III Reverse Transcriptase, by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and three gel slices corresponding to fragments in the ranges of 40-200 nt, 200-400 nt, and 400-600 nt were cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to rnpB nascent RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 5.5 μl nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, and 100 U SuperScript® III Reverse Transcriptase, by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range of 40-300 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg PGCGROWTHCONDITIONS
2 μg of RNA from the cytoplasmic fraction were diluted in 20 μl of Fragmentation buffer, and fragmented by incubation at 95°C for 5 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns. End repair of RNA fragments was performed in a final volume of 20 μl, in the presence of 20 U T4 Polynucleotide Kinase (NEB, cat. M0201L), and 20 U SUPERase• In™ RNase Inhibitor, by incubation at 37°C for 1 hour. End-repaired RNA was purified again using RNA Clean & Concentrator™-5 columns, and eluted in 6 μl of nuclease-free water. 6 μl of 2X RNA Loading Dye were added to end-repaired RNA. RNA was heated to 95°C for 2 minutes, and immediately placed on ice. Samples were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments above 200 nt was cut. The gel slice was crushed by centrifugation through a punctured 0.5 ml tube, and resuspended in 500 μl of Diffusion buffer supplemented with 60 U SUPERase• In™ RNase Inhibitor, then rotated at 4°C for 16 hours to allow passive diffusion of RNA fragments into buffer. RNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction, Replicate #1 PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction, Replicate #2 PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction, Replicate #1 PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction, Replicate #2 PGCGROWTHCONDITIONS
A single colony of Escherichia coli was inoculated into 250 ml of LB medium without antibiotics, and grown at 37C with shaking (150 RPM) for approximately 4 hours, until OD600 was ~0.3 (log phase). EDTA was then added to a final concentration of 1 mM, and incubated for additional 5 minutes to make bacteria permeable to Actinomycin D. Actinomycin D was then added to a final concentration of 5  g PGCGROWTHCONDITIONS
DMS-seq (Ribo- RNA) PGCGROWTHCONDITIONS
DMS-seq (Total RNA) PGCGROWTHCONDITIONS
Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. At this stage the solution clears considerably without increasing its viscosity, and nucleoid becomes visible. Using a cut P1000 pipette tip, the whole sample was gently layered on the top of a 5-30% w PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. All the relevant SPET-seq data (nascent RNA) analysis and normalization steps were performed using a custom wrapper built on top of the RNA Framework13. Briefly, reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome to extract transcripts’ sequences. Forward and reverse reads were independently mapped to the reference transcriptome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5 [--norc for forward reads, --nofw for reverse reads]). Forward and reverse mapped reads were then re-paired. Using reverse read mapping positions (corresponding to RNA Polymerase positions along gene), forward reads were split into separate SAM files for each transcription intermediate. When analysis was performed in deciles of transcription, genes were split into 10 equally sized deciles, and reads belonging to transcription intermediates falling in the same decile were pooled. SAM files were then passed to the rf-count tool of the RNA Framework to generate RT-stop counts (RC) files. Resulting RC files were normalized using the rf-norm tool of the RNA Framework in 50 nt sliding windows, with a 25 nt offset (parameters: -sm 2 -nm 2 -ec 0 -mc 0 -n 50 -nw 50 -wo 25). Mapping of DMS-seq data (mature RNA) was performed by using the rf-count tool (parameters: -cl 15 -bm 7 -ba -b5 5). Resulting RC files were normalized using the rf-norm tool (parameters: -sm 2 -nm 2 -ec 50 -mc 50 -n 50 -nw 50 -wo 25). The rf-norm tool generates a XML file for each transcript (or for each transcription intermediate PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. All the relevant SPET-seq data (nascent RNA) analysis and normalization steps were performed using a custom wrapper built on top of the RNA Framework13. Briefly, reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Forward and reverse reads were independently mapped to the RNase P (rnpB) gene using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5 [--norc for forward reads, --nofw for reverse reads]). Forward and reverse mapped reads were then re-paired. Using reverse read mapping positions (corresponding to RNA Polymerase positions along gene), forward reads were split into separate SAM files for each transcription intermediate. SAM files were then passed to the rf-count tool of the RNA Framework to generate RT-stop counts (RC) files, that were then normalized using the rf-norm tool. PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. Reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome. Reads were mapped to the reference genome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5). PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
In vitro transcription reactions were performed in a final volume of 50 µl. Each reaction contained 2 µl E. coli RNA Polymerase Holoenzyme (NEB, cat. M0551S), 5 µl E. coli RNA Polymerase Buffer (10X), 1 µl SUPERase• In™ RNase Inhibitor (Ambion, cat. AM2696), and 500 ng template DNA. Reactions were incubated at 37°C for 5 minutes to allow formation of the RNA Polymerase-DNA binary complex. Transcription was started by addition of 1 µl NTPs (25 mM each), and incubated at 37°C for 5 minutes. Transcription was stopped by addition of 1 µl DNase I (50 U PGCGROWTHCONDITIONS
library strategy: 3'-end RNA-seq PGCGROWTHCONDITIONS
library strategy: DMS-seq PGCGROWTHCONDITIONS
library strategy: SPET-seq PGCGROWTHCONDITIONS
molecule subtype: In vitro synthesized RNase P (rnpB) RNA PGCGROWTHCONDITIONS
molecule subtype: Total RNA (Cytosolic fraction) PGCGROWTHCONDITIONS
molecule subtype: Total RNA (Nucleoid fraction) PGCGROWTHCONDITIONS
OTHER PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified on RNA Clean & Concentrator™-5 columns following manufacturer’s instructions, and eluted in 6 μl of nuclease-free water. 6 μl of 2X RNA Loading Dye (ThermoScientific, cat. R0641) were added to purified RNA. Both DMS treated and untreated samples were heated at 95°C for 2 minutes, and immediately placed on ice. Samples were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice ranging from 50 nt to the full-length product was cut. Gel slices were crushed by centrifugation through a punctured 0.5 ml tube, and resuspended in 500 μl of Diffusion buffer [500 mM Ammonium acetate; 0.05% SDS] supplemented with 60 U SUPERase• In™ RNase Inhibitor, then rotated at 4°C for 16 hours to allow passive diffusion of RNA fragments into buffer. RNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg PGCGROWTHCONDITIONS
rnpB SPET-seq (in vitro) PGCGROWTHCONDITIONS
SPET-seq (Ribo- RNA) PGCGROWTHCONDITIONS
SPET-seq (Ribo- RNA), Replicate #1 PGCGROWTHCONDITIONS
SPET-seq (Ribo- RNA), Replicate #2 PGCGROWTHCONDITIONS
SPET-seq (Total RNA) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
substr: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework's (http: PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework's (http: PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework's (http: PGCGROWTHCONDITIONS
10A_MG+PMA_t60 PGCGROWTHCONDITIONS
10B_MG+PMA_t60 PGCGROWTHCONDITIONS
10C_MG+PMA_t60 PGCGROWTHCONDITIONS
1A_MG_t0 PGCGROWTHCONDITIONS
1B_MG_t0 PGCGROWTHCONDITIONS
1C_MG_t0 PGCGROWTHCONDITIONS
2A_MG_t10 PGCGROWTHCONDITIONS
2B_MG_t10 PGCGROWTHCONDITIONS
2C_MG_t10 PGCGROWTHCONDITIONS
3A_MG_t30 PGCGROWTHCONDITIONS
3B_MG_t30 PGCGROWTHCONDITIONS
3C_MG_t30 PGCGROWTHCONDITIONS
4A_MG_t60 PGCGROWTHCONDITIONS
4B_MG_t60 PGCGROWTHCONDITIONS
4C_MG_t60 PGCGROWTHCONDITIONS
5A_MG+Hg_t10 PGCGROWTHCONDITIONS
5B_MG+Hg_t10 PGCGROWTHCONDITIONS
5C_MG+Hg_t10 PGCGROWTHCONDITIONS
6A_MG+Hg_t30 PGCGROWTHCONDITIONS
6B_MG+Hg_t30 PGCGROWTHCONDITIONS
6C_MG+Hg_t30 PGCGROWTHCONDITIONS
7A_MG+Hg_t60 PGCGROWTHCONDITIONS
7B_MG+Hg_t60 PGCGROWTHCONDITIONS
7C_MG+Hg_t60 PGCGROWTHCONDITIONS
8A_MG+PMA_t10 PGCGROWTHCONDITIONS
8B_MG+PMA_t10 PGCGROWTHCONDITIONS
8C_MG+PMA_t10 PGCGROWTHCONDITIONS
9A_MG+PMA_t30 PGCGROWTHCONDITIONS
9B_MG+PMA_t30 PGCGROWTHCONDITIONS
9C_MG+PMA_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https: PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http: PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t10 PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t30 PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t60 PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t10 PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t30 PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t60 PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t0 PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t10 PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t30 PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
5min after UVtreatment 1, 40J, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
5min untreatedcells, 25 ug total RNA PGCGROWTHCONDITIONS
60min after UVtreatment 1, 40J, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
60min untreatedcells, 25 ug total RNA PGCGROWTHCONDITIONS
60min UV treated cells, 25 ug total RNA PGCGROWTHCONDITIONS
60min UVtreatment control, MG1655 in Davis+0.4%glu PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_12h_rep1 PGCGROWTHCONDITIONS
MT_12h_rep2 PGCGROWTHCONDITIONS
MT_24h_rep1 PGCGROWTHCONDITIONS
MT_24h_rep2 PGCGROWTHCONDITIONS
MT_48h_rep1 PGCGROWTHCONDITIONS
MT_48h_rep2 PGCGROWTHCONDITIONS
MT_6h_rep1 PGCGROWTHCONDITIONS
MT_6h_rep2 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_12h_rep1 PGCGROWTHCONDITIONS
WT_12h_rep2 PGCGROWTHCONDITIONS
WT_24h_rep1 PGCGROWTHCONDITIONS
WT_24h_rep2 PGCGROWTHCONDITIONS
WT_48h_rep1 PGCGROWTHCONDITIONS
WT_48h_rep2 PGCGROWTHCONDITIONS
WT_6h_rep1 PGCGROWTHCONDITIONS
WT_6h_rep2 PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 1min rep6 PGCGROWTHCONDITIONS
evolved 1min rep8 PGCGROWTHCONDITIONS
evolved 5min rep6 PGCGROWTHCONDITIONS
evolved 5min rep8 PGCGROWTHCONDITIONS
evolved 9min rep6 PGCGROWTHCONDITIONS
evolved 9min rep7 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 genotype: wild-type gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
t7 strain: wild type PGCGROWTHCONDITIONS
time: 1 min post-infection PGCGROWTHCONDITIONS
time: 5 min post-infection PGCGROWTHCONDITIONS
time: 9 min post-infection PGCGROWTHCONDITIONS
WT 1min rep7 PGCGROWTHCONDITIONS
WT 9min rep7 PGCGROWTHCONDITIONS
WT 9min rep8 PGCGROWTHCONDITIONS
3XSCOTS cDNA 24 h post-infection PGCGROWTHCONDITIONS
3XSCOTS cDNA in RPMI medium PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained 24 h post-infection PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained 2h post-infection PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained 8h post-infection PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained 8h post-infection  PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained after 8h post-infection PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained in RPMI  PGCGROWTHCONDITIONS
3XSCOTS cDNA obtained in RPMI medium PGCGROWTHCONDITIONS
After backgroud correction and total intensity normalization, ratio to reference were calculated and log base 2 transformed PGCGROWTHCONDITIONS
EDL933 24 h post infection in THP-1 humans cells PGCGROWTHCONDITIONS
EDL933 8h post-infection in THP-1 human cells PGCGROWTHCONDITIONS
EDL933 8h post THP-1 infection PGCGROWTHCONDITIONS
EDL933 cDNA 24 h post-infcetion of THP-1 human cells PGCGROWTHCONDITIONS
EDL933 cDNA obtained 24 h post- infection of THP-1 human cells PGCGROWTHCONDITIONS
EDL933 cDNA obtained 24h post-infection of THP-1 human cells PGCGROWTHCONDITIONS
EDL933 from overnight culture in LB broth PGCGROWTHCONDITIONS
EDL933 genomic DNA PGCGROWTHCONDITIONS
EDL933 genomic DNA  PGCGROWTHCONDITIONS
EDL933 genommic DNA PGCGROWTHCONDITIONS
EDL933 infection of THP-1 cells, recovered 2 h post-infection PGCGROWTHCONDITIONS
EDL933 infection of THP-1 cells, recovered 2h post-infection PGCGROWTHCONDITIONS
EDL933 in humans macrophages 8h post-infection PGCGROWTHCONDITIONS
EDL933 in RPMI medium PGCGROWTHCONDITIONS
EDL933 in THP-1 cells 8h post-infection PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genomic DNA E. coli EDL933 PGCGROWTHCONDITIONS
Genomic DNA from EDL933 PGCGROWTHCONDITIONS
Genomic DNA of EDL933 PGCGROWTHCONDITIONS
Genomic DNA was extracted by standard phenol-chloroform method (Sambrook, J, Molecular Cloning, 3rd Edition) PGCGROWTHCONDITIONS
Reference DNA genomic DNA PGCGROWTHCONDITIONS
Reference genomic DNA PGCGROWTHCONDITIONS
REference genomic DNA PGCGROWTHCONDITIONS
RPMI 1A, Microarray #1 first duplicate PGCGROWTHCONDITIONS
RPMI 1B, Microarray #1 second replicate PGCGROWTHCONDITIONS
RPMI 2A, Microarray #2, first replicate PGCGROWTHCONDITIONS
RPMI 2B, Microarray #2 second replicate PGCGROWTHCONDITIONS
T24 THP-1 infection, Microarray #1 first replicate PGCGROWTHCONDITIONS
T24 THP-1 infection, Microarray #1 second replicate PGCGROWTHCONDITIONS
T24 THP-1 infection, Microarray #2 first replicate PGCGROWTHCONDITIONS
T24 THP-1 infection, Microarray #2 second replicate PGCGROWTHCONDITIONS
T2 THP-1 infection, Microarray #1 first replicate PGCGROWTHCONDITIONS
T2 THP-1 infection, Microarray #1 second replicate PGCGROWTHCONDITIONS
T2 THP-1 infection, Microarray #2 first replicate PGCGROWTHCONDITIONS
T2 THP-1 infection, Microarray #2 second replicate PGCGROWTHCONDITIONS
T8 THP-1 infection, Microarray #1 first replicate PGCGROWTHCONDITIONS
T8 THP-1 infection, Microarray #1 second replicate PGCGROWTHCONDITIONS
T8 THP-1 infection, Microarray #2 first replicate PGCGROWTHCONDITIONS
T8 THP-1 infection, Microarray #2 second replicate PGCGROWTHCONDITIONS
TRIzol reagent (Gibco BRL) was used according to the manufacturer instruction. RNA was treated with DNase (Ambion). RNA sample was converted to cDNA in 5 independent reverse-transcription reactions as described previously (Graham, J. 1999. PNAS 96:11554-559). Bacterial transcript were purified from host transcript by using 3 round of the SCOTS procedure (Daigle, F. 2002. Methods Enzymol. 358:108-122). PGCGROWTHCONDITIONS
Data were analyzed with RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method. PGCGROWTHCONDITIONS
E. coli CRP N strain_acetate_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP N strain_acetate_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP N strain_acetate_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP N strain_acetate_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP N strain_glucose_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP N strain_glucose_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP N strain_glucose_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP N strain_glucose_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP N strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP Q strain_acetate_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP Q strain_acetate_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP Q strain_acetate_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP Q strain_acetate_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP Q strain_glucose_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP Q strain_glucose_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP Q strain_glucose_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP Q strain_glucose_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP Q strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP R strain_acetate_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP R strain_acetate_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP R strain_acetate_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP R strain_acetate_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP R strain_glucose_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP R strain_glucose_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP R strain_glucose_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli CRP R strain_glucose_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli CRP R strain grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli Wild type_acetate_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli Wild type_acetate_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli Wild type_acetate_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli Wild type_acetate_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli Wild type and its mutants were grown in M9 minimal medium with 10mM glucose or 30mM acetate as sole carbon source. Samples for RNA extraction were taken in middle exponential phase (OD600≈0.5) and in stationary phase (OD600≈1.5) PGCGROWTHCONDITIONS
E. coli Wild type_glucose_exponential phase_repl1 PGCGROWTHCONDITIONS
E. coli Wild type_glucose_exponential phase_repl2 PGCGROWTHCONDITIONS
E. coli Wild type_glucose_stationary phase_repl1 PGCGROWTHCONDITIONS
E. coli Wild type_glucose_stationary phase_repl2 PGCGROWTHCONDITIONS
E. coli wt grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli wt grown in acetate batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli wt grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli wt grown in acetate batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep1 PGCGROWTHCONDITIONS
E. coli wt grown in glucose batch minimal media, cells were harvested at exponential phase, biological rep2 PGCGROWTHCONDITIONS
E. coli wt grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep1 PGCGROWTHCONDITIONS
E. coli wt grown in glucose batch minimal media, cells were harvested at stationary phase, biological rep2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
genotyp PGCGROWTHCONDITIONS
Total RNA extraction using Vantage™ RNA Purification Kit (Origene, Rockville, MD, USA) was performed according with the manufacter instructions.  Purity and concentration of isolated RNA were assessed in a NanoDrop One spectrophotometer (Thermo Scientific Incorporated, WI, USA). Quality was evaluated by microfluidic capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, USA). PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
AR1- PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype PGCGROWTHCONDITIONS
growth phase: Late exponential PGCGROWTHCONDITIONS
K100Q PGCGROWTHCONDITIONS
K100Q rep 1 PGCGROWTHCONDITIONS
K100Q rep 2 PGCGROWTHCONDITIONS
K100Q rep 3 PGCGROWTHCONDITIONS
K100R PGCGROWTHCONDITIONS
K100R rep 1 PGCGROWTHCONDITIONS
K100R rep 2 PGCGROWTHCONDITIONS
K100R rep 3 PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
WT rep 1 PGCGROWTHCONDITIONS
WT rep 2 PGCGROWTHCONDITIONS
WT rep 3 PGCGROWTHCONDITIONS
Affymetrix Microarray Suite 5.0 PGCGROWTHCONDITIONS
Dilution rate = 0.14 PGCGROWTHCONDITIONS
E.coli_0%tannin_#2 PGCGROWTHCONDITIONS
E.coli_0%tannin_#8 PGCGROWTHCONDITIONS
E.coli_1%tannin_#3 PGCGROWTHCONDITIONS
e.coli_1%tannin_#5 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli BW13711 grown anaerobically in continuous culture in MOPS medium plus 0.4% glucose with 1% Acacia mearnsii condensed tannins.  PGCGROWTHCONDITIONS
Escherichia coli BW13711 grown anaerobically in continuous culture in MOPS medium plus 0.4% glucose without Acacia mearnsii condensed tannins.  PGCGROWTHCONDITIONS
Escherichia coli BW13711 grown anaerobically in continuous culture in MOPS medium plus 0.4% glucose without Acacia mearnsii condensed tannins.   PGCGROWTHCONDITIONS
Escherichia coli continous culture without tannins PGCGROWTHCONDITIONS
Escherichia coli continuous culture with 1% tannins PGCGROWTHCONDITIONS
Escherichia coli with 1% tannins PGCGROWTHCONDITIONS
Incubation temperature = 37C PGCGROWTHCONDITIONS
pH = 5.3 PGCGROWTHCONDITIONS
pH = 5.7 PGCGROWTHCONDITIONS
Promega RNase-free DNase PGCGROWTHCONDITIONS
Qiagen Rneasy mini kit PGCGROWTHCONDITIONS
50 bp single-end reads, were mapped to the genome with using bowtie2(Langmead and Salzberg, 2012) using default parameters. Alignments with bowtie2 mapping quality values lower than 40 were not retained for further analysis, leaving 128,413,654 and 76,508,335 reads. PGCGROWTHCONDITIONS
E. coli 3' RACE Rep1 PGCGROWTHCONDITIONS
E. coli 3' RACE Rep2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
In order to distinguish between 3’ ends of transient products of RNA metabolism and stable 3’ ends, we developed an algorithm to call coverage peaks. The algorithm will be discussed in detail in an upcoming manuscript, and the scripts used are available upon request from the authors. In short, positions in the E. coli genome were considered in descending order of coverage and assigned a p-value based on a Poisson distribution parameterized by the mean coverage of all covered bases in the genome. Peaks were rejected if their p-values exceeded 1e-4 or if there existed a >10-bp window containing the peak in which all positions were within 2-fold coverage of the peak position. Parameters were chosen based on analysis of annotated 3’ ends as well as qualitative analysis of peaks. This resulted in 20,019 peaks. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BIGWIG file containing coverage tracks from 3' RACE data PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: GFF file containing 3' end annotations PGCGROWTHCONDITIONS
total DNaseI treated RNA was depleted of ribosomal RNA using the Ribo-Zero™ RNA removal kit for Gram-negative bacteria (Epicentre). A 3' RNA adapter, based on the Illumina multiplexing adapter sequence (Oligonucleotide sequences © 2007-2014 Illumina, Inc. All rights reserved) blocked at the 3' end with an inverted dT (5'-GAUCGGAAGAGCACACGUCU[idT]-3'), was phosphorylated at the 5' end using T4 PNK (New England Biolabs) per the manufacturer’s protocol. The 3' RNA adapter was ligated to the 3' ends of the rRNA depleted RNA using T4 RNA ligase I (New England Biolabs). 1.5 mg of RNA was incubated at 20°C for 6 hours in 1X T4 RNA ligase reaction buffer with 1 mM ATP, 30 µM 3' RNA adapter, 10 % DMSO, 10 U of T4 RNA ligase I, and 40 U of RNasin (Promega) in a 20 ml reaction. RNA was then fragmented in equivalents of 100 ng using the RNA fragmentation reagents (Ambion®) per the manufacturer’s protocol at 70°C for 3 min and subsequently phosphorylated at the 5' ends using T4 PNK (New England Biolabs) per the manufacturer’s protocol to allow for ligation of the 5' adapter. RNA was size-selected (≈ 150-300 nt) and purified over a denaturing 8 % polyacrylamide PGCGROWTHCONDITIONS
Total RNA was isolated using the hot phenol method as described in (Lybecker et al., 2014). PGCGROWTHCONDITIONS
0x58 replicate 2 state 1 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 2 state 2 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 2 state 3 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 2 state 4 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 2 state 5 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 2 state 6 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 2 state 7 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 2 state 8 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 3 state 1 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 3 state 2 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 3 state 3 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 3 state 4 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 3 state 5 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 3 state 6 (IPTG+ PGCGROWTHCONDITIONS
0x58 replicate 3 state 7 (IPTG- PGCGROWTHCONDITIONS
0x58 replicate 3 state 8 (IPTG+ PGCGROWTHCONDITIONS
Control pAN1201 replicate 1 (IPTG- PGCGROWTHCONDITIONS
Control pAN1201 replicate 2 (IPTG- PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
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
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg PGCGROWTHCONDITIONS
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
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'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
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
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
BW25113 luxS LB 30C free-living cells 100 uM AI2 3h PGCGROWTHCONDITIONS
BW25113 luxS LB 30C free-living cells no AI2 for 3h PGCGROWTHCONDITIONS
BW25113 luxS LB 37C free-living cells 100 uM AI2 3h PGCGROWTHCONDITIONS
BW25113 luxS LB 37C free-living cells no AI2 3h PGCGROWTHCONDITIONS
BW25113 sdiA LB 30C OD 4.0 free-living cells PGCGROWTHCONDITIONS
BW25113 sdiA mutant LB with 1 mM indole 7-h 30C biofilm cell PGCGROWTHCONDITIONS
BW25113 sdiA mutant LB with DMF 7-h 30C biofilm cell PGCGROWTHCONDITIONS
BW25113 tnaA Biofilm 100 uM indole 7h LB 30C PGCGROWTHCONDITIONS
BW25113 tnaA Biofilm 100 uM indole 7h LB 37C PGCGROWTHCONDITIONS
BW25113 tnaA Biofilm DMF 7h LB 37C PGCGROWTHCONDITIONS
BW25113 tnaA LB 30C biofilm cells with DMF 7h PGCGROWTHCONDITIONS
BW25113 w PGCGROWTHCONDITIONS
Channel 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting PGCGROWTHCONDITIONS
MAS 5.0 Expression Analysis Default Setting. PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and 100 uM indole at 37ºC PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and DMF at 30ºC PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and DMF at 37ºC PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 BW25113 tnaA mutant after 7 hours of growth in LB with glasswool and with 100 uM indole at 30ºC PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 BW25113 w PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 sdiA mutant after 7 hours of growth in LB with glasswool at 30ºC with 1 mM indole presence. PGCGROWTHCONDITIONS
RNA extracted from biofilm cells of E. coli K-12 sdiA mutant after 7 hours of growth in LB with glasswool at 30ºC with DMF presence. PGCGROWTHCONDITIONS
RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 30ºC in LB, 100 uM AI2 was added in and 3-h further incubation was applied) PGCGROWTHCONDITIONS
RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 30ºC in LB, no AI2 was added in and 3-h further incubation was applied) PGCGROWTHCONDITIONS
RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 37ºC in LB, 100 uM AI2 was added in and 3-h further incubation was applied) PGCGROWTHCONDITIONS
RNA extracted from free living cells of E. coli K-12 BW25113 luxS mutant (when growth to OD600 0.5 at 37ºC in LB, no AI2 was added in and 3-h further incubation was applied) PGCGROWTHCONDITIONS
RNA extracted from free living cells of E. coli K-12 BW25113 sdiA mutant when growth to OD600 4.0 at 30ºC in LB PGCGROWTHCONDITIONS
RNA extracted from free living cells of E. coli K-12 BW25113 wild type when growth to OD600 4.0 at 30ºC in LB PGCGROWTHCONDITIONS
RNA extracted from suspension cells of E. coli K-12 BW25113 w PGCGROWTHCONDITIONS
The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) to OD600 0.5, 100 uM AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) to OD600 0.5, no AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) to OD600 4.0, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 37°C with shaking (250 rpm) to OD600 0.5, 100 uM AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (0.25 ml) was used to inoculate 25 ml of fresh LB medium. After incubation at 37°C with shaking (250 rpm) to OD600 0.5, no AI-2 was added in. after further 3-h incubation, 2.0 ml of cell culture was removed and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium. After incubation at 30°C with shaking (250 rpm) for 7 hours, 2.0 ml of cell culture was removed from suspension part and cells were pelleted and frozen in -80C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and 1 mM indole for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and DMF for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and DMF for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104). PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and DMF for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and with 100 uM indole for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) and with 100 uM indole for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 30°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) PGCGROWTHCONDITIONS
10_ESBL019 Filamented Repl 3 PGCGROWTHCONDITIONS
11_ESBL019 Transition Repl 3 PGCGROWTHCONDITIONS
12_ESBL019  Reverted Repl 3 PGCGROWTHCONDITIONS
13_ESBL019 Coliform Repl 4 PGCGROWTHCONDITIONS
14_ESBL019 Filamented Repl 4 PGCGROWTHCONDITIONS
15_ESBL019 Transition Repl 4 PGCGROWTHCONDITIONS
16_ESBL019  Reverted Repl 4 PGCGROWTHCONDITIONS
1_ESBL019 Coliform Repl 1 PGCGROWTHCONDITIONS
2_ESBL019 Filamented Repl 1 PGCGROWTHCONDITIONS
3_ESBL019 Transition Repl 1 PGCGROWTHCONDITIONS
4_ESBL019  Reverted Repl 1 PGCGROWTHCONDITIONS
5_ESBL019 Coliform Repl 2 PGCGROWTHCONDITIONS
6_ESBL019 Filamented Repl 2 PGCGROWTHCONDITIONS
75th percentile shift normalisation and baseline adjusted PGCGROWTHCONDITIONS
7_ESBL019 Transition Repl 2 PGCGROWTHCONDITIONS
8_ESBL019  Reverted Repl 2 PGCGROWTHCONDITIONS
9_ESBL019 Coliform Repl 3 PGCGROWTHCONDITIONS
ESBL019 Coliform PGCGROWTHCONDITIONS
ESBL019 Filamented PGCGROWTHCONDITIONS
ESBL019  Reverted PGCGROWTHCONDITIONS
ESBL019 Transition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four morphologic states of ESBL019 were used during the experiments. A first ESBL019 morphological state was prepared by resuspension of ESBL019 in cell culture medium (CCM) without ceftibuten supplementation prior to its inoculation of primary human bladder epithelial cells (HBEP) (designated; ESBL019 Coliform). A second ESBL019 morphological state was prepared by resuspension in CCM and then used to inoculate HBEP cells with ceftibuten supplementation (480ng PGCGROWTHCONDITIONS
morphology: Coliform PGCGROWTHCONDITIONS
morphology: Filamented PGCGROWTHCONDITIONS
morphology: Reverted (reverted back from a Filamented shape into a coli shape) PGCGROWTHCONDITIONS
morphology: Transition (from Coli into Filamented) PGCGROWTHCONDITIONS
RNA isolation was performed using an RNeasy mini kit (Qiagen Technologies, Hilden, Germany), according to the manufacturer’s protocol. DNA decontamination treatment was performed using Turbo DNase (Qiagen) and the quantity and purity of the purified RNA samples were determined using a spectrophotometer Nanodrop-1000 (Nanodrop Technologies Inc., Wilmington, DE, USA) by measuring the absorbance (A260, 230, 280) and calculating absorbance ratios (A260 PGCGROWTHCONDITIONS
strain: beta-lactamase (ESBL)-producing UPEC (ESBL019) PGCGROWTHCONDITIONS
The E. coli isolate ESBL019 was originally isolated from a patient at Örebro University hospital, Sweden and was maintained on tryptic soy agar (TSA) (Becton Dickinson, Le Pont Claix, France). ESBL019 was grown in Luria broth (Difco Laboratories, Detroit, MI, USA) overnight on shake at 200 rpm 37 °C prior to experiments. The bacteria were resuspended in sterile phosphate buffered saline prior to inoculation of CnT-21 cell culture medium (CCM) with or without ceftibuten (480 ng PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
lexA 10' after UV vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 10 min after UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA 20' after NOuv vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 20' after UV vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 20 min after NOuv, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA 20 min after UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA 40' after UV vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 40 min after UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA 5' after UV vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 5 min after UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA 60' after NOuv vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 60' after UV vs. 0', MG1655 PGCGROWTHCONDITIONS
lexA 60 min after NOuv, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA 60 min after UV treatment, 25 ug total RNA, 2 ug pdN6 PGCGROWTHCONDITIONS
lexA vs. wt, before UV treatment, MG1655 PGCGROWTHCONDITIONS
untreated cells, 25 ug total RNA PGCGROWTHCONDITIONS