<?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 = GSE65641
!Series_title = Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [ChIP-seq]
!Series_geo_accession = GSE65641
!Series_status = Public on Apr 18 2018
!Series_submission_date = Feb 04 2015
!Series_last_update_date = Apr 18 2018
!Series_pubmed_id = 29394395
!Series_summary = The carbon metabolism in bacteria is regulated by two global TFs, CRP and Cra. While the regulon of CRP has been extensively studied, the complete definition of Cra has been missing. Thus, in vivo TF binding measurement with ChIP-exo and transcriptional expression measurement with RNA-seq for Cra was performed to define the Cra regulon.
!Series_overall_design = A total of six samples were analyzed. cra-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose, fructose, and acetate upto mid-log phase with biological duplicates.
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_contributor = Donghyuk,,Kim
!Series_contributor = Sang,W,Seo
!Series_sample_id = GSM1602341
!Series_sample_id = GSM1602342
!Series_sample_id = GSM1602343
!Series_sample_id = GSM1602344
!Series_sample_id = GSM1602345
!Series_sample_id = GSM1602346
!Series_sample_id = GSM2829281
!Series_sample_id = GSM2829282
!Series_sample_id = GSM2829283
!Series_sample_id = GSM2829284
!Series_sample_id = GSM2829285
!Series_sample_id = GSM2829286
!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/GSE65641/suppl/GSE65641_RAW.tar
!Series_platform_id = GPL16085
!Series_platform_taxid = 562
!Series_sample_taxid = 562
!Series_relation = SubSeries of: GSE65643
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA274574
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP053192
^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 = GSM1602341
!Sample_title = <Name>Cra glucose 1</Name>
!Sample_geo_accession = GSM1602341
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Feb 04 2015
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = cra-8myc tagged strain_glucose
!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>cra-8myc-tagged</Gtype>
!Sample_characteristics_ch1 = cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log</Phase>
!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_growth_protocol_ch1 = E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_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_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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!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/SAMN03329440
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX865351
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1602nnn/GSM1602341/suppl/GSM1602341_cra_glucose_1.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM1602342
!Sample_title = <Name>Cra glucose 2</Name>
!Sample_geo_accession = GSM1602342
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Feb 04 2015
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = cra-8myc tagged strain_glucose
!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>cra-8myc-tagged</Gtype>
!Sample_characteristics_ch1 = cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% glucose</Supp>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log</Phase>
!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_growth_protocol_ch1 = E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_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_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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!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/SAMN03329436
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX865352
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1602nnn/GSM1602342/suppl/GSM1602342_cra_glucose_2.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM1602343
!Sample_title = <Name>Cra fructose 1</Name>
!Sample_geo_accession = GSM1602343
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Feb 04 2015
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = cra-8myc tagged strain_fructose
!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>cra-8myc-tagged</Gtype>
!Sample_characteristics_ch1 = cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% fructose</Supp>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log</Phase>
!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_growth_protocol_ch1 = E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_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_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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!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/SAMN03329435
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX865353
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1602nnn/GSM1602343/suppl/GSM1602343_cra_fructose_1.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM1602344
!Sample_title = <Name>Cra fructose 2</Name>
!Sample_geo_accession = GSM1602344
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Feb 04 2015
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = cra-8myc tagged strain_fructose
!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>cra-8myc-tagged</Gtype>
!Sample_characteristics_ch1 = cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% fructose</Supp>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log</Phase>
!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_growth_protocol_ch1 = E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_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_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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!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/SAMN03329437
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX865354
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1602nnn/GSM1602344/suppl/GSM1602344_cra_fructose_2.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM1602345
!Sample_title = <Name>Cra acetate 1</Name>
!Sample_geo_accession = GSM1602345
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Feb 04 2015
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = cra-8myc tagged strain_acetate
!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>cra-8myc-tagged</Gtype>
!Sample_characteristics_ch1 = cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% acetate</Supp>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log</Phase>
!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_growth_protocol_ch1 = E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_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_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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!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/SAMN03329438
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX865355
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1602nnn/GSM1602345/suppl/GSM1602345_cra_acetate_1.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM1602346
!Sample_title = <Name>Cra acetate 2</Name>
!Sample_geo_accession = GSM1602346
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Feb 04 2015
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = cra-8myc tagged strain_acetate
!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>cra-8myc-tagged</Gtype>
!Sample_characteristics_ch1 = cultured in: <Med>M9 minimal media</Med> with <Supp>0.2% acetate</Supp>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log</Phase>
!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_growth_protocol_ch1 = E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_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_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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!Sample_description = Immunoprecipitated DNA
!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/SAMN03329439
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX865356
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1602nnn/GSM1602346/suppl/GSM1602346_cra_acetate_2.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM2829281
!Sample_title = <Name>RpoB WT 1</Name>
!Sample_geo_accession = GSM2829281
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Oct 24 2017
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Supp>acetate</Supp>
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype: <Gtype>Wildtype</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766)
!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 = 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.
!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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!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/SAMN07829462
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3316474
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2829nnn/GSM2829281/suppl/GSM2829281_rpob_wt_acetate_1.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM2829282
!Sample_title = <Name>RpoB WT 2</Name>
!Sample_geo_accession = GSM2829282
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Oct 24 2017
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Supp>acetate</Supp>
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype: <Gtype>Wildtype</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766)
!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 = 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.
!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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!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/SAMN07829461
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3316475
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2829nnn/GSM2829282/suppl/GSM2829282_rpob_wt_acetate_2.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM2829283
!Sample_title = <Name>RpoB ∆cra 1</Name>
!Sample_geo_accession = GSM2829283
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Oct 24 2017
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Supp>acetate</Supp>
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype: delta-<Gtype>cra Knock-out strain</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766)
!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 = 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.
!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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!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/SAMN07829460
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3316476
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2829nnn/GSM2829283/suppl/GSM2829283_rpob_delcra_acetate_1.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM2829284
!Sample_title = <Name>RpoB ∆cra 2</Name>
!Sample_geo_accession = GSM2829284
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Oct 24 2017
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Supp>acetate</Supp>
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype: delta-<Gtype>cra Knock-out strain</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766)
!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 = 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.
!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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!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/SAMN07829459
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3316477
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2829nnn/GSM2829284/suppl/GSM2829284_rpob_delcra_acetate_2.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM2829285
!Sample_title = <Name>RpoB ∆crp 1</Name>
!Sample_geo_accession = GSM2829285
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Oct 24 2017
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Supp>acetate</Supp>
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype: delta-<Gtype>crp Knock-out strain</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766)
!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 = 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.
!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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!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/SAMN07829458
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3316478
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2829nnn/GSM2829285/suppl/GSM2829285_rpob_delcrp_acetate_1.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0
^SAMPLE = GSM2829286
!Sample_title = <Name>RpoB ∆crp 2</Name>
!Sample_geo_accession = GSM2829286
!Sample_status = Public on Apr 18 2018
!Sample_submission_date = Oct 24 2017
!Sample_last_update_date = Apr 18 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Supp>acetate</Supp>
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype: delta-<Gtype>crp Knock-out strain</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-rpoB</Anti> (Santa Cruz Biotech, sc-56766)
!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 = 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.
!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 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.
!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
!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/SAMN07829457
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3316479
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2829nnn/GSM2829286/suppl/GSM2829286_rpob_delcrp_acetate_2.gff.gz
!Sample_series_id = GSE65641
!Sample_series_id = GSE65643
!Sample_data_row_count = 0

</gse>