<?xml version="1.0" encoding="UTF-8"?>

<gse xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="esquema-gcs.xsd">

^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE65710
!Series_title = Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [ChIP-seq]
!Series_geo_accession = GSE65710
!Series_status = Public on Aug 13 2015
!Series_submission_date = Feb 06 2015
!Series_last_update_date = Nov 16 2015
!Series_pubmed_id = 26279566
!Series_summary = Oxidative stress that originates from reactive oxygen species (ROS) is an inevitable consequence of aerobic respiration in bacteria. Three transcription factors (TFs), OxyR, SoxR, and SoxS play a critical role in transcriptional regulation of the defense system. However, the full genome-wide regulatory potential of them remains elusive. Here, we comprehensively reconstruct genome-wide OxyR, SoxR, and SoxS transcriptional regulatory networks in Escherichia coli under oxidative stress. Integrative data analysis reveals that OxyR, SoxR, and SoxS regulons are comprised of 38 genes in 28 transcription units (TUs), 11 genes in 10 TUs, and 34 genes in 25 TUs, respectively, significantly expanding the current knowledge of their regulatory networks. Comparison of them to other stress-response regulatory networks highlights minimal overlap between their regulons, indicating that E. coli has a series of relatively distinct stress responses covering the range of different stresses. We also demonstrate that these intricate networks coordinate detoxification process with DNA and protein damage repair, cell wall synthesis, divalent metal ion homeostasis, as well as metabolic robustness to produce overall response of E. coli to oxidative stress.
!Series_overall_design = 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.
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_contributor = Sang,W,Seo
!Series_contributor = Donghyuk,,Kim
!Series_sample_id = GSM1603380
!Series_sample_id = GSM1603381
!Series_sample_id = GSM1603382
!Series_sample_id = GSM1603383
!Series_sample_id = GSM1603384
!Series_sample_id = GSM1603385
!Series_contact_name = Donghyuk,,Kim
!Series_contact_email = donghyuk.kim@khu.ac.kr
!Series_contact_laboratory = Systems Biology Lab
!Series_contact_department = Department of Genetic Engineering
!Series_contact_institute = Kyung Hee University
!Series_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Series_contact_city = Yongin-si
!Series_contact_state = Gyeonggi-do
!Series_contact_zip/postal_code = 17104
!Series_contact_country = South Korea
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65710/suppl/GSE65710_RAW.tar
!Series_platform_id = GPL16085
!Series_platform_taxid = 562
!Series_sample_taxid = 562
!Series_relation = SubSeries of: GSE65712
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA275134
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP053437
^PLATFORM = GPL16085
!Platform_title = Illumina MiSeq (Escherichia coli)
!Platform_geo_accession = GPL16085
!Platform_status = Public on Sep 20 2012
!Platform_submission_date = Sep 20 2012
!Platform_last_update_date = Sep 20 2012
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Escherichia coli
!Platform_taxid = 562
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM1603380
!Sample_title = <Name>OxyR PQ 1</Name>
!Sample_geo_accession = GSM1603380
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = oxyR-8myc-tagged_PQ treated
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>oxyR-8myc</Gtype>-tagged
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti>
!Sample_characteristics_ch1 = chip antibody vendor: Santa Cruz Biotech
!Sample_characteristics_ch1 = chip antibody cat. #: sc-28207
!Sample_treatment_protocol_ch1 = 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.
!Sample_growth_protocol_ch1 = A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!Sample_data_processing = library strategy: ChIP-seq (ChIP-exo)
!Sample_data_processing = ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
!Sample_data_processing = MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
!Sample_data_processing = Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
!Sample_data_processing = For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
!Sample_data_processing = Genome_build: <Gversion>ASM584v2</Gversion>
!Sample_data_processing = 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(.).
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339598
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871621
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1603nnn/GSM1603380/suppl/GSM1603380_oxyr_pq1.gff.gz
!Sample_series_id = GSE65710
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603381
!Sample_title = <Name>OxyR PQ 2</Name>
!Sample_geo_accession = GSM1603381
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = oxyR-8myc-tagged_PQ treated
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>oxyR-8myc</Gtype>-tagged
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti>
!Sample_characteristics_ch1 = chip antibody vendor: Santa Cruz Biotech
!Sample_characteristics_ch1 = chip antibody cat. #: sc-28207
!Sample_treatment_protocol_ch1 = 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.
!Sample_growth_protocol_ch1 = A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!Sample_data_processing = library strategy: ChIP-seq (ChIP-exo)
!Sample_data_processing = ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
!Sample_data_processing = MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
!Sample_data_processing = Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
!Sample_data_processing = For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
!Sample_data_processing = Genome_build: <Gversion>ASM584v2</Gversion>
!Sample_data_processing = 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(.).
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339597
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871622
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1603nnn/GSM1603381/suppl/GSM1603381_oxyr_pq2.gff.gz
!Sample_series_id = GSE65710
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603382
!Sample_title = <Name>SoxR PQ 1</Name>
!Sample_geo_accession = GSM1603382
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = soxR-8myc-tagged_PQ treated
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>soxR-8myc</Gtype>-tagged
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti>
!Sample_characteristics_ch1 = chip antibody vendor: Santa Cruz Biotech
!Sample_characteristics_ch1 = chip antibody cat. #: sc-28207
!Sample_treatment_protocol_ch1 = 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.
!Sample_growth_protocol_ch1 = A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!Sample_data_processing = library strategy: ChIP-seq (ChIP-exo)
!Sample_data_processing = ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
!Sample_data_processing = MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
!Sample_data_processing = Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
!Sample_data_processing = For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
!Sample_data_processing = Genome_build: <Gversion>ASM584v2</Gversion>
!Sample_data_processing = 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(.).
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339606
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871623
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1603nnn/GSM1603382/suppl/GSM1603382_soxr_pq1.gff.gz
!Sample_series_id = GSE65710
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603383
!Sample_title = <Name>SoxR PQ 2</Name>
!Sample_geo_accession = GSM1603383
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = soxR-8myc-tagged_PQ treated
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>soxR-8myc</Gtype>-tagged
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti>
!Sample_characteristics_ch1 = chip antibody vendor: Santa Cruz Biotech
!Sample_characteristics_ch1 = chip antibody cat. #: sc-28207
!Sample_treatment_protocol_ch1 = 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.
!Sample_growth_protocol_ch1 = A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!Sample_data_processing = library strategy: ChIP-seq (ChIP-exo)
!Sample_data_processing = ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
!Sample_data_processing = MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
!Sample_data_processing = Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
!Sample_data_processing = For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
!Sample_data_processing = Genome_build: <Gversion>ASM584v2</Gversion>
!Sample_data_processing = 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(.).
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339607
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871624
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1603nnn/GSM1603383/suppl/GSM1603383_soxr_pq2.gff.gz
!Sample_series_id = GSE65710
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603384
!Sample_title = <Name>SoxS PQ 1</Name>
!Sample_geo_accession = GSM1603384
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = soxS-8myc-tagged_PQ treated
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>soxS-8myc</Gtype>-tagged
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti>
!Sample_characteristics_ch1 = chip antibody vendor: Santa Cruz Biotech
!Sample_characteristics_ch1 = chip antibody cat. #: sc-28207
!Sample_treatment_protocol_ch1 = 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.
!Sample_growth_protocol_ch1 = A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!Sample_data_processing = library strategy: ChIP-seq (ChIP-exo)
!Sample_data_processing = ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
!Sample_data_processing = MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
!Sample_data_processing = Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
!Sample_data_processing = For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
!Sample_data_processing = Genome_build: <Gversion>ASM584v2</Gversion>
!Sample_data_processing = 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(.).
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339600
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871625
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1603nnn/GSM1603384/suppl/GSM1603384_soxs_pq1.gff.gz
!Sample_series_id = GSE65710
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603385
!Sample_title = <Name>SoxS PQ 2</Name>
!Sample_geo_accession = GSM1603385
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = soxS-8myc-tagged_PQ treated
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>soxS-8myc</Gtype>-tagged
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log phase</Phase> for <Supp>20 min</Supp>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti>
!Sample_characteristics_ch1 = chip antibody vendor: Santa Cruz Biotech
!Sample_characteristics_ch1 = chip antibody cat. #: sc-28207
!Sample_treatment_protocol_ch1 = 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.
!Sample_growth_protocol_ch1 = A total of six samples were analyzed. oxyR-8myc, soxR-8myc, and soxS-8myc tagged cells were cultured in <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!Sample_data_processing = library strategy: ChIP-seq (ChIP-exo)
!Sample_data_processing = ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
!Sample_data_processing = MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
!Sample_data_processing = Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
!Sample_data_processing = For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
!Sample_data_processing = Genome_build: <Gversion>ASM584v2</Gversion>
!Sample_data_processing = 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(.).
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339599
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871626
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1603nnn/GSM1603385/suppl/GSM1603385_soxs_pq2.gff.gz
!Sample_series_id = GSE65710
!Sample_series_id = GSE65712
!Sample_data_row_count = 0

</gse>