Data sets

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+
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+
+^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 = GSE54899
+!Series_title = Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [ChIP-Seq]
+!Series_geo_accession = GSE54899
+!Series_status = Public on Sep 09 2014
+!Series_submission_date = Feb 12 2014
+!Series_last_update_date = Dec 09 2014
+!Series_pubmed_id = 25222563
+!Series_summary = The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Polyomic data analysis revealed that a total of 81 genes in 42 transcription units (TUs) are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation as well as holo-Fur repression. We showed that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development was found. These results indicate that Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate E. coli responses to the availability of iron.
+!Series_overall_design = [ChIP-exo]:  A total of twelve samples were analyzed. WT and Fur-8-myc tagged cells were cultured in the presense and absence of iron with biological duplicates. To analyze static RNAP binding, rifampicin was also added to the media with biological duplicates. DPD = iron chelator.
+!Series_type = Genome binding/occupancy profiling by high throughput sequencing
+!Series_contributor = Sang Woo,,Seo
+!Series_contributor = Donghyuk,,Kim
+!Series_sample_id = GSM1326335
+!Series_sample_id = GSM1326336
+!Series_sample_id = GSM1326337
+!Series_sample_id = GSM1326338
+!Series_sample_id = GSM1326339
+!Series_sample_id = GSM1326340
+!Series_sample_id = GSM1326341
+!Series_sample_id = GSM1326342
+!Series_sample_id = GSM1326343
+!Series_sample_id = GSM1326344
+!Series_sample_id = GSM1326345
+!Series_sample_id = GSM1326346
+!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/GSE54nnn/GSE54899/suppl/GSE54899_RAW.tar
+!Series_platform_id = GPL17439
+!Series_platform_taxid = 511145
+!Series_sample_taxid = 511145
+!Series_relation = SubSeries of: GSE54901
+!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA238004
+!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP037710
+^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 = GSM1326335
+!Sample_title = Fur with Fe 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326335
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12 </Strain>substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>fur-8myc</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_growth_protocol_ch1 = <Orgn>E. coli</Orgn> <Strain>K-12</Strain> <Substrain>MG1655</Substrain> <Gtype>WT</Gtype> and <Gtype>Fur-8-myc </Gtype>tagged strains were grown to <Phase>mid-log phase </Phase><Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media </Med>supplemented with <Supp>0.2% glucose</Supp>. For <Supp>iron</Supp> treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for <Supp>DPD</Supp> treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the <Supp>rifampicin</Supp> dissolved in methanol was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913 </Gversion>genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640285
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469826
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326335/suppl/GSM1326335_chipexo_fur_fe1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326336
+!Sample_title = Fur with Fe 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326336
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>fur-8myc</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_growth_protocol_ch1 = <Orgn>E. coli</Orgn> <Strain>K-12</Strain> <Substrain>MG1655</Substrain> <Gtype>WT</Gtype> and <Gtype>Fur-8-myc</Gtype> tagged strains were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For <Supp>iron</Supp> treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for <Supp>DPD</Supp> treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the <Supp>rifampicin</Supp> dissolved in methanol was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640287
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469827
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326336/suppl/GSM1326336_chipexo_fur_fe2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326337
+!Sample_title = Fur with DPD 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326337
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli </Orgn>str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>fur-8myc</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: <Supp>DPD</Supp>
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640293
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469828
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326337/suppl/GSM1326337_chipexo_fur_dpd1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326338
+!Sample_title = Fur with DPD 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326338
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli </Orgn>str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>fur-8myc</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: <Supp>DPD</Supp>
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640284
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469829
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326338/suppl/GSM1326338_chipexo_fur_dpd2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326339
+!Sample_title = RpoB with Fe 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326339
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640286
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469830
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326339/suppl/GSM1326339_chipexo_rpob_fe1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326340
+!Sample_title = RpoB with Fe 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326340
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640292
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469831
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326340/suppl/GSM1326340_chipexo_rpob_fe2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326341
+!Sample_title = RpoB with Fe and rifampicin 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326341
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: <Supp>Fe and rifampicin</Supp>
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: <Technique>ChIP-exo</Technique>
+!Sample_data_processing = ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
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+!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
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+!Sample_contact_country = South Korea
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+!Sample_library_selection = ChIP
+!Sample_library_source = genomic
+!Sample_library_strategy = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640288
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469832
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+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_platform_id = GPL17439
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_platform_id = GPL17439
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_series_id = GSE54899
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+
+</gse>

+<?xml version="1.0" encoding="UTF-8"?>
+
+<gse xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="esquema-gcs.xsd">
+
+^DATABASE = GeoMiame
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+!Database_institute = NCBI NLM NIH
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+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
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+!Sample_platform_id = GPL17439
+!Sample_contact_name = Donghyuk,,Kim
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+!Sample_contact_city = Yongin-si
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+!Sample_contact_country = South Korea
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_platform_id = GPL17439
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+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640290
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469835
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326344/suppl/GSM1326344_chipexo_rpob_dpd2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326345
+!Sample_title = RpoB with DPD and rifampicin 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326345
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: WT
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: DPD and rifampicin
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640295
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469836
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326345/suppl/GSM1326345_chipexo_rpob_dpd_rif1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326346
+!Sample_title = RpoB with DPD and rifampicin 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326346
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: WT
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: DPD and rifampicin
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640294
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469837
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326346/suppl/GSM1326346_chipexo_rpob_dpd_rif2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326347
+!Sample_title = WT with Fe 1 (RNA-seq)
+!Sample_geo_accession = GSM1326347
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to <Phase>mid-log phase</Phase> <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. For <Supp>iron</Supp> treated cells, <Supp>0.1mM of FeCl2</Supp> were treated from the beginning of culture, and for <Supp>DPD</Supp> treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640298
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469838
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326348
+!Sample_title = WT with Fe 2 (RNA-seq)
+!Sample_geo_accession = GSM1326348
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
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+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640297
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469839
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326349
+!Sample_title = WT with DPD 1 (RNA-seq)
+!Sample_geo_accession = GSM1326349
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = agent: <Supp>DPD</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640301
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469840
+!Sample_supplementary_file_1 = NONE
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+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326350
+!Sample_title = WT with DPD 2 (RNA-seq)
+!Sample_geo_accession = GSM1326350
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
+!Sample_characteristics_ch1 = agent: <Supp>DPD</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640300
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469841
+!Sample_supplementary_file_1 = NONE
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+!Sample_series_id = GSE54901
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+^SAMPLE = GSM1326351
+!Sample_title = Δfur with Fe 1 (RNA-seq)
+!Sample_geo_accession = GSM1326351
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
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+!Sample_source_name_ch1 = Total RNA isolated from E. coli
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+!Sample_taxid_ch1 = 511145
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+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640296
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469842
+!Sample_supplementary_file_1 = NONE
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+!Sample_series_id = GSE54901
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+^SAMPLE = GSM1326352
+!Sample_title = Δfur with Fe 2 (RNA-seq)
+!Sample_geo_accession = GSM1326352
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
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+!Sample_taxid_ch1 = 511145
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+!Sample_characteristics_ch1 = agent: <Supp>Fe</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640299
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469843
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326353
+!Sample_title = Δfur with DPD 1 (RNA-seq)
+!Sample_geo_accession = GSM1326353
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>Δfur</Gtype>
+!Sample_characteristics_ch1 = agent: <Supp>DPD</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640303
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469844
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326354
+!Sample_title = Δfur with DPD 2 (RNA-seq)
+!Sample_geo_accession = GSM1326354
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: <Gtype>Δfur</Gtype>
+!Sample_characteristics_ch1 = agent: <Supp>DPD</Supp>
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = <Technique>RNA-Seq</Technique>
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640302
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469845
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+
+</gse>

+<?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 = GSE54899
+!Series_title = Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [ChIP-Seq]
+!Series_geo_accession = GSE54899
+!Series_status = Public on Sep 09 2014
+!Series_submission_date = Feb 12 2014
+!Series_last_update_date = Dec 09 2014
+!Series_pubmed_id = 25222563
+!Series_summary = The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Polyomic data analysis revealed that a total of 81 genes in 42 transcription units (TUs) are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation as well as holo-Fur repression. We showed that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development was found. These results indicate that Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate E. coli responses to the availability of iron.
+!Series_overall_design = [ChIP-exo]:  A total of twelve samples were analyzed. WT and Fur-8-myc tagged cells were cultured in the presense and absence of iron with biological duplicates. To analyze static RNAP binding, rifampicin was also added to the media with biological duplicates. DPD = iron chelator.
+!Series_type = Genome binding/occupancy profiling by high throughput sequencing
+!Series_contributor = Sang Woo,,Seo
+!Series_contributor = Donghyuk,,Kim
+!Series_sample_id = GSM1326335
+!Series_sample_id = GSM1326336
+!Series_sample_id = GSM1326337
+!Series_sample_id = GSM1326338
+!Series_sample_id = GSM1326339
+!Series_sample_id = GSM1326340
+!Series_sample_id = GSM1326341
+!Series_sample_id = GSM1326342
+!Series_sample_id = GSM1326343
+!Series_sample_id = GSM1326344
+!Series_sample_id = GSM1326345
+!Series_sample_id = GSM1326346
+!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/GSE54nnn/GSE54899/suppl/GSE54899_RAW.tar
+!Series_platform_id = GPL17439
+!Series_platform_taxid = 511145
+!Series_sample_taxid = 511145
+!Series_relation = SubSeries of: GSE54901
+!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA238004
+!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP037710
+^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 = GSM1326335
+!Sample_title = Fur with Fe 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326335
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: fur-8myc
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: Fe
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640285
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469826
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326335/suppl/GSM1326335_chipexo_fur_fe1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326336
+!Sample_title = Fur with Fe 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326336
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: fur-8myc
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: Fe
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640287
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469827
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326336/suppl/GSM1326336_chipexo_fur_fe2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326337
+!Sample_title = Fur with DPD 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326337
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: fur-8myc
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: DPD
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640293
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469828
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326337/suppl/GSM1326337_chipexo_fur_dpd1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326338
+!Sample_title = Fur with DPD 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326338
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: fur-8myc
+!Sample_characteristics_ch1 = chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)
+!Sample_characteristics_ch1 = agent: DPD
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640284
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469829
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326338/suppl/GSM1326338_chipexo_fur_dpd2.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326339
+!Sample_title = RpoB with Fe 1 (ChIP-exo)
+!Sample_geo_accession = GSM1326339
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Immunoprecipitated DNA
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: WT
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: Fe
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640286
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469830
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326339/suppl/GSM1326339_chipexo_rpob_fe1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326340
+!Sample_title = RpoB with Fe 2 (ChIP-exo)
+!Sample_geo_accession = GSM1326340
+!Sample_status = Public on Sep 09 2014
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+!Sample_molecule_ch1 = genomic DNA
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+</gse>

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+xsi:noNamespaceSchemaLocation="esquema-gcs.xsd">
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_platform_id = GPL17439
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+!Sample_contact_email = donghyuk.kim@khu.ac.kr
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+!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
+!Sample_contact_city = Yongin-si
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+!Sample_contact_country = South Korea
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+!Sample_library_strategy = ChIP-Seq
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+!Sample_molecule_ch1 = genomic DNA
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+!Sample_data_processing = library strategy: ChIP-exo
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+!Sample_platform_id = GPL17439
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+!Sample_molecule_ch1 = genomic DNA
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+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640291
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469834
+!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1326nnn/GSM1326343/suppl/GSM1326343_chipexo_rpob_dpd1.gff.gz
+!Sample_series_id = GSE54899
+!Sample_series_id = GSE54901
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+!Sample_geo_accession = GSM1326344
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
+!Sample_type = SRA
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+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: DPD
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+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
+!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 = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640290
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469835
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+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
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+!Sample_type = SRA
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+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: WT
+!Sample_characteristics_ch1 = chip antibody: anti-RpoB (Neoclone, WP002)
+!Sample_characteristics_ch1 = agent: DPD and rifampicin
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+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
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+!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
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+!Sample_library_selection = ChIP
+!Sample_library_source = genomic
+!Sample_library_strategy = ChIP-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640295
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469836
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+!Sample_series_id = GSE54899
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+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 10 2014
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+!Sample_molecule_ch1 = genomic DNA
+!Sample_extract_protocol_ch1 = ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = library strategy: ChIP-exo
+!Sample_data_processing = ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters  -S
+!Sample_data_processing = Genome_build: ASM584v2
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+!Sample_platform_id = GPL17439
+!Sample_contact_name = Donghyuk,,Kim
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+!Sample_contact_institute = Kyung Hee University
+!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
+!Sample_contact_city = Yongin-si
+!Sample_contact_state = Gyeonggi-do
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+!Sample_contact_country = South Korea
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+!Sample_library_strategy = ChIP-Seq
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+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469837
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+!Sample_title = WT with Fe 1 (RNA-seq)
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+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
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+!Sample_molecule_ch1 = total RNA
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+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
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+!Sample_platform_id = GPL17439
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+!Sample_contact_department = Department of Genetic Engineering
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+!Sample_contact_city = Yongin-si
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+!Sample_contact_country = South Korea
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+!Sample_status = Public on Sep 09 2014
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+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
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+!Sample_platform_id = GPL17439
+!Sample_contact_name = Donghyuk,,Kim
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+!Sample_contact_city = Yongin-si
+!Sample_contact_state = Gyeonggi-do
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+!Sample_contact_country = South Korea
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+!Sample_molecule_ch1 = total RNA
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+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
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+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
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+!Sample_molecule_ch1 = total RNA
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+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
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+!Sample_molecule_ch1 = total RNA
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+!Sample_contact_state = Gyeonggi-do
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+!Sample_status = Public on Sep 09 2014
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+!Sample_characteristics_ch1 = agent: Fe
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = RNA-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640299
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469843
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326353
+!Sample_title = Δfur with DPD 1 (RNA-seq)
+!Sample_geo_accession = GSM1326353
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: Δfur
+!Sample_characteristics_ch1 = agent: DPD
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = RNA-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640303
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469844
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+^SAMPLE = GSM1326354
+!Sample_title = Δfur with DPD 2 (RNA-seq)
+!Sample_geo_accession = GSM1326354
+!Sample_status = Public on Sep 09 2014
+!Sample_submission_date = Feb 12 2014
+!Sample_last_update_date = Sep 09 2014
+!Sample_type = SRA
+!Sample_channel_count = 1
+!Sample_source_name_ch1 = Total RNA isolated from E. coli
+!Sample_organism_ch1 = Escherichia coli str. K-12 substr. MG1655
+!Sample_taxid_ch1 = 511145
+!Sample_characteristics_ch1 = genotype/variation: Δfur
+!Sample_characteristics_ch1 = agent: DPD
+!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
+!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h.
+!Sample_molecule_ch1 = total RNA
+!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
+!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
+!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
+!Sample_data_processing = Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v.1.3.0
+!Sample_data_processing = Genome_build: ASM584v2
+!Sample_data_processing = Supplementary_files_format_and_content: Comma-delimited text file includes RPKM values for each Sample.
+!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 = cDNA
+!Sample_library_source = transcriptomic
+!Sample_library_strategy = RNA-Seq
+!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02640302
+!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX469845
+!Sample_supplementary_file_1 = NONE
+!Sample_series_id = GSE54900
+!Sample_series_id = GSE54901
+!Sample_data_row_count = 0
+
+</gse>