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<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 = GSE66441
!Series_title = Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq]
!Series_geo_accession = GSE66441
!Series_status = Public on Aug 11 2015
!Series_submission_date = Mar 02 2015
!Series_last_update_date = Aug 13 2015
!Series_pubmed_id = 26258987
!Series_summary = The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons are comprised of 45 genes in 31 transcription units (TUs), significantly expanding the current knowledge of the GadEWX regulatory network. We demonstrate that GadEWX directly and coherently regulate several proton efflux/influx and generating/consuming enzymes with pairs of negative-feedback loops to maintain pH homeostasis by controlling proton flow. In addition, GadEWX regulate genes with assorted functions including molecular chaperones, acid resistance, stress response, and other regulatory activities. These results present a comprehensive understating on how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress.
!Series_overall_design = A total of six samples were analyzed. GadE-8-myc, GadW-8 -myc, and GadX-8-myc tagged cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_contributor = Sang,W,Seo
!Series_contributor = Donghyuk,,Kim
!Series_sample_id = GSM1622463
!Series_sample_id = GSM1622464
!Series_sample_id = GSM1622465
!Series_sample_id = GSM1622466
!Series_sample_id = GSM1622467
!Series_sample_id = GSM1622468
!Series_sample_id = GSM1633277
!Series_sample_id = GSM1633278
!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/GSE66nnn/GSE66441/suppl/GSE66441_RAW.tar
!Series_platform_id = GPL17439
!Series_platform_taxid = 511145
!Series_sample_taxid = 511145
!Series_relation = SubSeries of: GSE66482
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA276918
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP055726
^PLATFORM = GPL17439
!Platform_title = Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)
!Platform_geo_accession = GPL17439
!Platform_status = Public on Jul 12 2013
!Platform_submission_date = Jul 12 2013
!Platform_last_update_date = Jul 12 2013
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Escherichia coli str. K-12 substr. MG1655
!Platform_taxid = 511145
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM1622463
!Sample_title = <Name>ChIP-exo GadE pH5.5 1</Name>
!Sample_geo_accession = GSM1622463
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 02 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>gadE-8myc</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03382528
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX894213
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1622nnn/GSM1622463/suppl/GSM1622463_chipexo_gadE_ph5.5_1.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1622464
!Sample_title = <Name>ChIP-exo GadE pH5.5 2</Name>
!Sample_geo_accession = GSM1622464
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 02 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>gadE-8myc</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03382526
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX894214
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1622nnn/GSM1622464/suppl/GSM1622464_chipexo_gadE_ph5.5_2.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1622465
!Sample_title = <Name>ChIP-exo GadW pH5.5 1</Name>
!Sample_geo_accession = GSM1622465
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 02 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>gadW-8myc</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03382527
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX894215
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1622nnn/GSM1622465/suppl/GSM1622465_chipexo_gadW_ph5.5_1.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1622466
!Sample_title = <Name>ChIP-exo GadW pH5.5 2</Name>
!Sample_geo_accession = GSM1622466
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 02 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>gadW-8myc</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03382529
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX894216
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1622nnn/GSM1622466/suppl/GSM1622466_chipexo_gadW_ph5.5_2.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1622467
!Sample_title = <Name>ChIP-exo GadX pH5.5 1</Name>
!Sample_geo_accession = GSM1622467
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 02 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>gadX-8myc</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03382530
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX894217
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1622nnn/GSM1622467/suppl/GSM1622467_chipexo_gadX_ph5.5_1.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1622468
!Sample_title = <Name>ChIP-exo GadX pH5.5 2</Name>
!Sample_geo_accession = GSM1622468
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 02 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>gadX-8myc</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03382531
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX894218
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1622nnn/GSM1622468/suppl/GSM1622468_chipexo_gadX_ph5.5_2.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1633277
!Sample_title = <Name>ChIP-exo RpoS pH5.5 1</Name>
!Sample_geo_accession = GSM1633277
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 12 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>WT</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-RpoS</Anti> (neoclone, WP009)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03402346
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX955681
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1633nnn/GSM1633277/suppl/GSM1633277_chipexo_rpoS_ph5.5_1.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1633278
!Sample_title = <Name>ChIP-exo RpoS pH5.5 2</Name>
!Sample_geo_accession = GSM1633278
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 12 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Immunoprecipitated DNA
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>WT</Gtype>
!Sample_characteristics_ch1 = chip antibody: <Anti>anti-RpoS</Anti> (neoclone, WP009)
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!Sample_molecule_ch1 = genomic DNA
!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 = GPL17439
!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/SAMN03402347
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX955682
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1633nnn/GSM1633278/suppl/GSM1633278_chipexo_rpoS_ph5.5_2.gff.gz
!Sample_series_id = GSE66441
!Sample_series_id = GSE66482
!Sample_data_row_count = 0

</gse>