"strain: K-12 MG1655"	"characteristics_ch1.1"
"genotype/variation: soxR-8myc-tagged"	"characteristics_ch1.2"
"treated with: 250 uM of paraquat at mid-log phase for 20 min"	"characteristics_ch1.3"
"chip antibody: anti-myc"	"characteristics_ch1.4"
"chip antibody vendor: Santa Cruz Biotech"	"characteristics_ch1.5"
"chip antibody cat. #: sc-28207"	"characteristics_ch1.6"
"library strategy: ChIP-seq (ChIP-exo)"	"data_processing.1"
"ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S"	"data_processing.2"
"MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping."	"data_processing.3"
"Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity."	"data_processing.4"
"For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity."	"data_processing.5"
"Genome_build: ASM584v2"	"data_processing.6"
"Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.)."	"data_processing.7"
"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."	"extract_protocol_ch1.1"
"ChIP-seq libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"soxR-8myc-tagged_PQ treated"	"source_name_ch1.1"
"SoxR PQ 1"	"title.1"
"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."	"treatment_protocol_ch1.1"
"ChIP-Seq"	"library_strategy.1"
"strain: K-12 MG1655"	"characteristics_ch1.1"
"genotype/variation: soxR-8myc-tagged"	"characteristics_ch1.2"
"treated with: 250 uM of paraquat at mid-log phase for 20 min"	"characteristics_ch1.3"
"chip antibody: anti-myc"	"characteristics_ch1.4"
"chip antibody vendor: Santa Cruz Biotech"	"characteristics_ch1.5"
"chip antibody cat. #: sc-28207"	"characteristics_ch1.6"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"soxR-8myc-tagged_PQ treated"	"source_name_ch1.1"
"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."	"treatment_protocol_ch1.1"